The actual beginning of the millennium, with the beginning of the 2001st year AD of the Julian calendar system, in spite of the misunderstanding of many people, who think that the millennium began a year earlier.

Surekill.  At night a man, Carleton Chase, runs up to a payphone on a city street in Worcester, Mass. He leaves a message on an answering machine, saying to call "him" off and give Chase a chance to explain. He runs off and enters a police station. Another man is seen following him. Chase is frantic and officers put him in a holding cell after he tries to grab an officer's gun. He screams that he is not safe in the cell, then through the door window the officers see blood splatter.

Scully looks at an x-ray - the man was shot by an armor piercing bullet. She and Doggett eventually determine that the gun was fired through the roof of the police station, but it was an impossibly lucky shot because there was no way for the shooter to see to target his victim. A woman, Tammi, enters the office of AAA Surekill Exterminators. She plays the answering machine message and hears the message, in which Chase says to check the right desk drawer. Tammi looks in the drawer and finds her record book in a lock box, but she is interrupted by her boss, Dwight Cooper. Dwight's brother, Randall, also works there and is the man who we saw following Chase. Outside, near a dumpster, Dwight asks Randall what happened last night. Randall found Chase stealing. Dwight says Randall has to get the money before doing "his thing." They are going out again that night.

Doggett and Scully visit Chase's real estate office. He did a lot of business with the exterminating company. In a back room, Doggett finds a .45 shell - not the same caliber as the bullet that killed Chase. The room has several bullet holes in the walls. That night, Dwight enters a warehouse where three men, apparently drug dealers, are working. Dwight wants the pile of money they have on the table and they fall from bullet wounds, fired through the wall by Randall. The next day, Scully and Doggett visit the scene with police. Outside the room where the men died are bullet holes that perfectly match up with the victims. Scully speculates that someone with exceptional vision might have the ability to see at wavelengths that allow targeting through the walls. Doggett isn't impressed with the thought of "X-ray vision."

At the Surekill office, Dwight calls Tammi into a room for a tryst. As she undresses she says she doesn't like having Randall right outside. Randall watches intently through the wall but is distracted when Scully and Doggett walk in. Dwight comes out to talk with them. Dwight says has been legally blind since birth. The agents ask Dwight about the bills found Chase's office. On a piece of fabric found at the police station, apparently from a cloth wrapped around the gun to silence it, was soaked in pesticide chemicals. Dwight served jail time a long time ago, but he and his brother are chamber of commerce members now. The agents ask why Chase called their office a few minutes before he was murdered. Dwight says they had all gone home and there was no message on their machine. After the agents leave, Dwight asks Tammi about the message and she claims that she accidentally erased it before listening. Dwight peers into Tammi's eyes, holding up a lighter flame to see clearly by, saying that by seeing her eyes he can see the truth.

Doggett finds the record of Dwight's 1986 arrest for grand theft auto. Since he is blind, Dwight must have had a driver. Randall was also arrested at the same time, but didn't serve much time. The two brothers are twins. At home that night, Randall and Tammi are in adjoining apartments. He watches her through the walls as she undresses and prepares for bed. The next day, Tammi gets to work early and rushes in to learn what is inside the desk drawer. She finds a lock box, but Dwight and Randall interrupt her. They take the box and as they begin to open it, Doggett and several police officers enter with a search warrant. Doggett opens the box but finds it empty. Scully, however, finds several file folders which result in Dwight and Randall being taken in for questioning. Their little company billed over Chase for over $700,000. Dwight and Randall are looking at each other through the questioning room walls. Scully asks Randall point black whether he can see through the wall. She speculates that he shoots drug dealers through walls then takes their money, right? Randall says he's just an exterminator. Scully says she thinks it's all Dwight's idea and that it's time for Randall to think for himself.

The agents then question Tammi together - she claims she just keeps the books and didn't know about the murders. The agents think that Chase was the fence and that he was killed because of a relationship between him and Tammi. While the agents question Tammi, the brothers agree that Tammi is a problem that they have to take care of. Tammi is not under arrest and goes home. In Tammi's phone records the agents find several late night calls to chase. Tammi goes next door - she tells Randall she knows it was him that killed Chase. He has tender feeling toward her and she apparently reciprocates.

The next day, at a bus station, Tammi tells Randall that she needs the book Randall took out of the box to protect her from Dwight. He gives it to her and the book has a key in it. She tells Randall she will be back in a half hour and drives off. The agents visit Tammi's apartment - her clothes are gone and she is apparently running. Doggett checks her phone and determines that her last call was to the bus company. Tammi has picked up the money from a bank safe deposit box and gets back into her car. Dwight is in the back seat. Police arrive at the bus station and Randall slips away. At the Surekill office, Dwight discovers that Tammi has been keeping two sets of books and has stolen $100,000. Tammi claims that Chase was blackmailing her, and making her "do things," the implication of which is sexual. Randall killed Carleton because of what he was doing to Tammi. Randall arrives back at the office. Dwight wants Randall to kill Tammi, taunting him that Tammi used him. Dwight tells Randall that blood is thicker than anything, and leaves the room so that Randall can kill her. She pleads for her life as Randall wraps a cloth around the gun to silence it. He aims and shoots - but shoots through the wall and kills Dwight.

At the police station, Randall has declined representation. Tammi has not been found. Scully muses that Randall could look at anything in the world and looked at her - maybe he say something that she didn't even see in herself. Doggett replies that if he saw into her heart, they're out of FBI territory. The episode ends with Randall looking through the wall at the computer display of Tammi's picture.

Salvage.  Nora and Carl mourn for Nora's husband, Ray, who recently died. Carl was a co-worker and they say that Ray got sick because he fought in the Gulf War. As Carl drives off, he is surprised to find a man standing in the middle of the street. The car hits him and seems to split around him, as if the man was an immovable mass of metal. Ray is injured but through the broken window, he sees Ray, who he thought was dead. Ray reaches for Carl and Carl screams.

Scully and Doggett are at the scene. The engine compartment of the car is split, but the body of the driver is not in the car. The object hit by the car would have to be hundreds of times as sense as steel, the agents indicate. As the car is lifted up by a wrecker, there are what appear to be footprints under the engine compartment. Nora comes up and is distressed. Doggett talks with her until Scully calls him over - she has found Carl's body. It has holes in the forehead that look like finger holes poked in clay. The autopsy shows that the body was pulled through the windshield and that there are five holes in the skull that match up with the positions of five fingers of a human hand. Meanwhile, a fingerprint and blood are found at the scene that are identified as Ray's and were clearly not left before Ray died.

Ray wakes up in a halfway house. He goes to a mirror and uses nail clippers to remove individual hairs of his beard. When they fall into the sink they are like little bits of wire. Doggett goes to Nora's home. Harvey is also there. He owns a salvage yard and was both Ray's and Carl's employer. Ray's body was to be cremated, but Doggett's research found no record of the cremation. Doggett wonders if Ray might possibly still be alive. Harvey says that Ray was a good man who couldn't walk or even lift his head just before he died. Meanwhile, Ray is eating in a common room of the halfway house. Larina approaches, saying that she helps out at the halfway house and offers to talk, if he wants. He rebuffs her, but not before she notices that he is eating the aluminum foil wrapping, along with the sandwich inside.

In the auto salvage yard, Ray spray paints some waste barrels blue, then goes inside his office to feed several invoices through a shredding machine. Ray enters the room. Harvey fires a gun at him and Ray is propelled backwards through a glass door. Harvey finds a severed hand with what appears to be metal growing out of the stump. Ray, missing an arm, walks up and Harvey screams.

Doggett studies Harvey's body. There is blue paint around Harvey's fingernails. He sees that Harvey was shredding papers, and it is clear that someone "took a hit" from the shotgun. It is hard to imagine that someone injured by the shotgun that way could then kill Harvey. Doggett finds that one page in the shredder is only partially shredded, allowing him to read the invoice. Ray is back at the halfway house, cleaning himself. The wounds of the shotgun pellets look like metal rather than injured skin. Larina enters his room - people saw blood on him when he came in and she wants to help, but he orders her out. Doggett visits Chamber Technologies, the company on the partially shredded invoice. Dr. David Clifton, whose name is on the invoice, is no longer employed there. A scientist who is Clifton's successor says that all of Clifton's work was conceptual, developing "smart metals" that can rebuild themselves. They certainly always dispose of waste legally.

Scully concludes that Ray's entire cellular structure had been transformed by being exposed to something. Doggett says that a "metal man" only happens in movies, to which Scully says, "does it?" Norina hears the news report about Harry's murder and telephone's Ray's home. Scully gets blood tests back. It was certainly Ray's blood, but it has enough metal alloy in the blood to kill an elephant. It doesn't make sense to Doggett. Ray had been treated for substance abuse but turned his life around, met Nora and got married. He's the kind of guy you want to cheer for, not a murderer. Scully counters that even if they can find him, who is to say that they can stop him.

The scientist is at his computer at Chamber Technologies. Ray enters and the scientist lures Ray into a test chamber. The door slams shot and locks, and Doggett and Scully rush in with a SWAT team. It was a setup to trap Ray. Ray begins pounding on the four-inch metal walls, but soon the pounding stops and the agents realize that Ray has escaped through another wall. Scully looks closely on blood left on the jagged metal where Ray escaped. The blood is turning itself into metal. As they take the scientist away to safety, Doggett notices that several hazardous waste barrels at Chamber Technologies are painted blue.

Ray returns to his room and Nora is waiting for him. She can't understand why he didn't contact her, but he says, "I'm not me." He shows her that his body is turning to metal and he wants to make the people who did it to him pay. At the salvage yard, Doggett examines some blue waste drums he noticed earlier. You can still see some of the Chambers company logo that Harvey painted over. Doggett tips over a barrel and a body spills out, looking strangely metallic. It is Dr. Clifton. Questioning Clifton's replacement at Chamber Technologies, they learn that Clifton had been working on an alloy that had genetic material in it, to give it memory and allow it to repair itself. He knew he was dying but nobody knew what would happen to his body. The waste barrels were supposed to go to a proper disposal facility. Doggett sees Nora down the hall and checks to see what she is doing at the office of her supposedly dead husband. She is on the phone to Ray, but Doggett interrupts her. She confesses that she was looking for the name of who was responsible but says she didn't have time to give the name to Ray.

A swat team raids the halfway house. Ray suffocates Larina in order to keep her from giving him away. Later, Doggett and Scully tell Nora about Ray killing Larina. They take Nora home and watch the house, but Ray slips in. When he leaves, Nora runs outside saying that Ray made her give him the name she found. The name is Owen Harris. Ray intercepts Harris' car, as he did with Curt, except that Harris gets the car stopped before hitting Ray. Ray pulls Harris outside and Harris pleads that he's just an accountant, why is Ray doing this. Harris' children in the car cry in terror.

Later, Doggett and Scully drive up. Harris is being treated by an ambulance team. Harris authorized sending the hazardous waste to the salvage yard, so he is responsible for Ray's condition. The agents don't understand why Ray ran away but it is clear to the audience that the fear in of the Harris children caused Ray to back off. Scully sums up that Ray's body died and what was left was not really a man, but maybe what saved Harris and his family was a flicker of humanity. In the final scene, we see a car being dropped into a crusher at a junk yard. Ray is inside the car, choosing to be crushed, too.

Notes: A newspaper mentions George Bush succeeding Bill Clinton as President, probably placing this episode in December or January. The reference to "Metal Men" is an in joke about Robert Patrick's role in the movie Terminator II.

Badlaa.  In India, a heavyset man in a suit, Hugh Potocki, enters a crowded airport -- he is going to America. Nearby is a beggar without legs, sitting on a wheeled platform. The man gives the beggar a few coins, but the beggar drops the coins. In the bathroom, the beggar comes in and the man is violently pulled out of the stall, under the stall door. Later, the man arrives in a Washington DC hotel room. The beggar's wheeled platform is among his luggage. After the bellboy leaves, the man sits on the bed and blood begins flowing from his body, his eyes red.

Scully and Doggett arrive at the hotel. The man was an importer from Minneapolis. Preliminary tests show nothing. The maid found the body 20 minutes after the bellboy left. One thing that the police missed the first time was a bloody handprint that appears to be that of a child. Neither agent is ready to believe that a child would be involved. At an elementary school in Maryland, a principal interviews a man for a job as a custodian, but viewers see that while the principal sees a European man, it is actually the Indian beggar sitting in the chair. In the autopsy, Scully finds massive abdominal tissue damage, but it's hard to tell whether something went in or out of the abdomen. Doggett suggests a drug smuggling connection, however it doesn't account for some of Scully's findings. Several indicators show that the body had been dead 24-36 hours when found, meaning he would have been dead before leaving India.

At the school, several boys get into a scuffle, including Trevor, who is in seventh grade and Quentin who is in sixth. Quinton's father, who is picking him up from school, breaks up the scuffle. The beggar is nearby but people see him as the custodian. Doggett finds a report from India that several days earlier, another American businessman was found dead in India under similar circumstances. Various documents show a 33-pound discrepancy in body weights before and after death. Both victims were big men. Scully asks what if whatever it is killed these men entered and exited of its own free will, living inside the victims as a stowaway of sorts. Doggett thinks the theory doesn't work. At night, Quinton sees a reflection of the beggar in a mirror in his bedroom. His dad tells him it wasn't real. The father goes downstairs and settles in to watch TV, and the beggar is on the floor near him. The Red-Headed Boy hears his father scream and goes downstairs to check. The father is still sitting in the chair, not moving, with his eyes red.

Scully and Doggett are at the Red-Headed Boy 's house. The father is dead. Quinton tells Scully that the person he saw was a "munchkin" -- a small person with no legs. Doggett finds the same small handprints and evidence that the person came in through a window. The father, however, has none of the abdomen damage of the other victims. Only the red eyes, caused by burst blood vessels, is similar. Scully does an autopsy and in the pathology lab finds that the father's stomach has swelled to a very large size. She dictates that she is doing an unauthorized procedure -- and cuts into the distended abdomen. When she makes the incision, a hand reaches out of the abdomen. Scully grabs her gun, but whatever it was in the stomach has disappeared, leaving blood and hand marks on the floor. She follows blood marks to a storage closet. She sees nothing inside, but viewers see the beggar.

The principal reprimands the custodian for being late for work. He gets out a wheeled pail for a mop, and Trevor sees the custodian's body, lit from behind by a doorway. The body is flickering. Scully and Doggett talk to Chuck Burks, who shows video he took in Indian in the 70s. Chuck can't figure out what is going on with this case. He describes a secret order of the occult having powers of the mind and the ability to manipulate reality. One of these mystics could make you believe that you cannot see him in a room, or disguise himself. Doggett asks and Chuck explains that he runs the advanced imaging lab at the University of Maryland, and says, "I dabble." Doggett isn't impressed. Trevor goes to Quinton's the home. Although they squabbled earlier, Trevor tells him. "I think I know who did it."

Chuck returns to the X-Files office to talk with Scully. She says she is just trying to see this case as Mulder would. The talk about the Indian mystics, who chuck says are very religious. Murder would endanger their eternal souls. What would cause them to break that faith? Maybe revenge? Scully shows a report of an American chemical plant that released a small cloud of gas six months ago. 118 people were killed. The father of one victim of that disaster is listed in records as a holy man of the beggar class. But if he is out for revenge, why is he killing the people that he is killing?

Trevor walks down the street and hears the sound of the casters on the beggar's platform, although he can't see anyone. He runs home. His mother follows him into the back yard and sees Trevor underwater in the swimming pool. She jumps in and discovers that the body is the beggar. Scully and Doggett, and other officials, are at Trevor's home. His mother is dead. As she is taken away, Scully and Doggett talk by the pool. Doggett doesn't know how the death fits into the case. It is close to another death and the woman's eyes are red, Scully says. Doggett questions Scully's methodology. She counters that there is a motive and a pattern that they can find, but not if they are fighting each other. Trevor comes home and claims that "the little man" was there and followed him.

The agents have the janitor in for questioning, based on Trevor's report. Chuck arrives. Doggett tells him that the man doesn't speak. Scully left after four hours of trying to interrogate him. Chuck sets up a video camera because he suspects that the man sitting there may not be as they see him. The video camera shows that nobody is in the chair where they clearly see the janitor. Doggett is befuddled, but realizes that if the man is not there, he could be anywhere.

Scully returns to Trevor's home because she has more questions for him. Doggett phones her cell phone to ask her to return. It turns out that Trevor isn't home, anyway. At the school at night, the principal sees the janitor. He doesn't speak. Knowing that he had been called in for questioning, the principal phones Scully. Trevor is at school watching the Janitor and communicating with Quinton by radio. Trevor follows the beggar and attempts to throw acid from a science storeroom on the Beggar, but as soon as the bottle drops, the beggar is not there. It doesn't work and the beggar is soon chasing Quinton through the school halls. In a classroom, he can't get windows open to escape. Trevor is outside the window and yells that he will get help. The beggar advances on Quinton. Scully and the principal enter and can't see the beggar, who has transformed into the appearance of Trevor. Quinton screams and pleads at Scully to shoot him. Scully can't bring herself to shoot. Doggett drives up and hears shots. Rushing into the classroom, he finds Scully and the principal with the dead beggar on the floor.

Later, Scully is still disturbed. Doggett sort of understands what happened. She shot a young boy. Doggett says that the good news is that she was wrong and it only appeared to be Trevor. Why did you shoot? Because of what the boy saw. Scully says that in an instant she realized that it is what Mulder would have seen or understood. She cries because she is not capably of having as open a mind as Mulder. Doggett says this whole thing doesn't make sense.

In the final scene of the episode, we see the same beggar in the airport in India.

The Gift.  A car drives down a country road in the rain. It drives up to a rural home in Pennsylvania. A man gets out and enters the house. Another man and woman are there, as is another man who looks like a Neanderthal, with sores and wounds on his face. The first man fires at a monster, then leaves. The man with the gun is Mulder. He gets back in his car and drives off. The scene is a flashback.

John Doggett drives in his car. He is remembering conversations about Mulder -- about Mulder's terminal sickness, and about Doggett's pledge to find Mulder. Doggett arrives at a Pennsylvania sheriff's office. The sheriff says Mulder was there in the spring, investigating a missing woman. It turned out to be a false report. The woman, named Marie, never left her house. Cell phone records show that Mulder was here the week before disappeared. Doggett and the Sheriff go to talk with Marie and her husband. the husband does most of the talking. Marie has kidney disease. Doggett knows that Mulder was investigating a statement Marie had made to her sister that she was about to disappear. She didn't want her sister to worry. The husband claims nothing happened. On Saturday May 6, Mulder came back, according to cell phone records. The husband denies that they saw Mulder again. There is a local folk legend about a creature that lives in the woods. Mulder twisted that into a theory that the creature was going to come and eat Marie alive.

Doggett sees three gunshot holes plastered over in the wall, but doesn't ask about them. Doggett searches Mulder's apartment and feeds the fish. He does a thorough search this time and finds a gun taped under the sink. Doggett and Skinner talk about the gun. The clip was three rounds short of being full. Mulder never filed a report on the case or on the discharge of his weapon. Tests done for Doggett have found micro blood spatters on the gun. Skinner is forceful that Mulder really did disappear. He denies that Mulder may have shot someone and them deliberately disappeared. Doggett feels that he can't ask Scully, because she signed case reports for Mulder, and thus could be implicated. Doggett, however, is not going to take it to OPR, i.e. the people who do internal FBI investigations. The sheriff has had a grave opened in the cemetery. The sheriff, with several other men, dogs and pickup trucks, drive up to a house where a blonde women lives. They give her two minutes to produce "it." As they wait, someone runs through the nearby woods. The men give chase and catch the man in a net. He struggles and makes sounds like an animal. The blonde woman pleads but they put the man into a cage on the back of a truck.

Doggett and Skinner arrive at the sheriff's office. They drove from Washington when they couldn't reach the Sheriff by phone. He misleads them and claims he was hunting. They ask about a death certificate of a unidentified transient, found on Sunday May 7. Doggett thinks everybody in the town is lying. The agents go the cemetery where the body was buried and find that the grave has been opened. Inside are the remains of a casket, but a hole in the bottom of the casket makes it appear that someone tunneled out of the grave. The sheriff goes to Marie's house where her husband is painting a circle and cross symbol in chicken blood. They agree that they have to move fast. Marie doesn't want to do that they want but is told she has no choice. The truck with the cage is outside and the man- animal is inside. Marie lies down on the floor and kisses her husband. He will be waiting for her. The sheriff opens the cage and we see the man-animal. It enters the house opens its mouth very wide and blood spatters. Later, Doggett and Skinner drive up to the house and interview Marie's husband. They speculate that the sheriff was there. Mulder came back here and shot someone, and they are all lying. They want to talk to Marie, but she is not there. Skinner finds blood on the floor. In a cave or underground passage, we see the man-animal on his knees, retching, and the vomit is shaped like a human body.

Police are now at Marie's house. Doggett is trying to understand what happened when Mulder returned. The man claims his wife coughed up the blood. Doggett concludes that Mulder was trying to protect Marie from the man who is supposed to be buried in the coffin. In UV light, officers they find the remains of the circle and cross symbol. Via Internet, the Lone Gunmen advise Doggett and Skinner that the symbol looks like a Native American medicine wheel. Legends date back for hundreds of years about a shaman who could be summoned by the wheel symbol to help the sick. Doggett sees a connection with Marie's kidney disease. He goes to see the blonde woman. She was the one who reported finding the body in the woods near her home in May. Doggett wants to know what the secret is that people are keeping. He recites his theory that Mulder thought it was some sort of soul eater. She tells him that he has it all backwards, and that there things have been this way for hundreds of years. He finds a cellar door and investigates. It leads deep underground to the caves and tunnels. Following them, he finds Marie's body, naked in a kind of goo. As he checks her, she awakes. He carries her out, wrapped in a blanket.

Doggett watches in the hospital as Marie's husband puts her wedding ring back on her. She is fine and her kidneys have healed. She is in perfect health. This "soul eater" actually took her to cure her, it seems. It is clear to Doggett that Mulder was not trying to protect Marie. Doggett returns to the blonde woman's home. She finally agrees to explain it to Doggett. This thing looks the way it does because it doesn't cure the disease, it consumes it. This is why it looks covered with sores and is in constant pain. Doggett realizes that Mulder came to try to save himself from his brain disease. First preparing to do the ritual himself, Mulder saw how it suffered and shot it to take its pain away. They buried it but it can't die. The blonde woman protected it in her home, but now that they know it's back, they will make it suffer again. The creature is there and Doggett begins to take it into protective custody, but the sheriff and his posse drive up. They won't let him take it. "We have sick people who need what he has," they say. In a confrontation, Doggett is shot through the chest and dies. The creature escapes and they bury Doggett's body. The blonde watches it all.

The man-animal brings Doggett back to life in the cave, absorbing the gunshot would. The blonde is in the cave beside the prostrate creature when Doggett awakes. It took Doggett's death, she says, and died itself. Doggett finally freed it. Back at the office, Doggett tries to write his case report, but he can't figure out how to start. Skinner compliments him that he got inside Mulder's head and understood what Mulder was doing. Skinner encourages Doggett to not submit a report. It would open up a world of trouble for Scully and take months to prove that Scully was not involved. Skinner and Doggett both know what happened. Skinner says nobody else needs to. Doggett imagines Mulder standing in the office, watching him.

Medusa.  A man is alone in a subway stop in Boston -- another man approaches, dressed in black. The first is an undercover cop, who describes the second into a hidden microphone. The second could be planning a mugging. The train arrives and the cop enters the car. The second man enters the car a few moments later from the rear. Suddenly, the train loses power and the breaks screech. The two men struggle and we hear screams. At the next stop, passengers find the body of the officer, his skull and portions of his body apparently eaten away, as if from acid.

At the Boston transit operations center, Scully and Doggett talk with authorities. The local transit supervisor is upset that one of the main subway arteries is closed and announces that the line must be open for the evening commute. One third of the dead man's body tissue was eaten away. Scully doesn't want the line reopened until they determine what caused the death. Transit police Lieutenant Bianco thinks it was an assailant, using acid or something. Doggett, Bianco, the man who was construction supervisor of the tunnel a few years earlier and a woman from the Centers for Disease Control don assault gear and enter the tunnel. Scully will remain in transit control and communicate by radio. Doggett also carries a small TV transmitter with a camera on his headset. Doggett acknowledges that Scully has the experience with this kind of matter. He is just tagging along. Ventilation was shut down, making the tunnel hot. The construction supervisor screams -- he has a burn on his neck. Liquid in a puddle a few yards back might contain acid. The woman from CDC does an instant test, but the puddle is only seawater that has seeped in.

The team sees movement -- there is someone else in the tunnel. The go find him. They pass a tunnel connection to an old, obsolete, about a mile from there the train lost power. Doggett has a hunch, and enters the tunnel. As the members of the team debate returning to the main tunnel, Doggett is attacked. Doggett is stunned, but soon wakes up. The assailant is the one responsible for the police officer's death and portions of his body apparently eaten away. Bianco pushes to leave, saying that they have found the man responsible for the death, but the Construction supervisor finds three bodies, wrapped in plastic. They have been there for some time and all show signs of the same tissue damage. There may be a contagion at work after all. The woman from CDC sees a shadow indicating that there is someone else in the tunnel, but they can't find the person. At Scully's direction, the team leaves the bodies and continues up the main tunnel. The construction supervisor screams again -- his arm is burning. Scully quickly orders them to pour fresh water on the burns, which is done from a canteen. Doggett and Bianco leave the woman from CDC to care for the construction supervisor, pending arrival of a quarantine team to be sent by Scully. Bianco sees a green glow on his hand, but does not report it.

Scully meets the hazardous chemical team as they remove the construction supervisor from the tunnels. The team also has the three bodies, and Scully prevents them from being taken away by transit workers. She suspects that the transit supervisor wants to cover up the problem, suspecting that he knew that the bodies were there. The bodies are taken to the CDC after all. Doggett and Bianco continue, and Doggett discovers the green fluorescent glow on the Bianco's face. It burns other people, but hasn't had any effect on the Bianco yet. Doggett has to pulls a gun on Bianco to keep him from leaving. They fight and Doggett is knocked down. A marine biologist comes to talk to Scully. She analyzed the salt-water sample. There are medusas -- a kind of microscopic jellyfish -- in the water. They glow with bioelectricity, but the bioelectricity does not burn people on contact. Something triggers it. In the tunnels we see that Doggett is unconscious and also has the green glow of the medusa on him.

Scully's repeated radio calls wake Doggett up. Lt. Bianco is not there. Doggett discovers the green glow on his skin. Scully wants to send a quarantine unit, but Doggett insists on stopping Bianco, in order to keep the medusa from spreading. The transit supervisor tells Scully that there are already passengers waiting on many platforms. They can't block the tunnels to keep Bianco in. Doggett finds Bianco, lying in the tunnel. Scully tells Doggett to get out, but Bianco asks him to stay. Doggett puts an arm under Bianco's shoulder and helps him walk. They see a shadow of another person. Doggett finds a child, a boy who points up the tunnel. He is uninfected. Scully thinks she has it figured out -- sweat may trigger the electrical burns. Sweat will conduct electricity and a child's sweat glands are not fully developed. Doggett follows the boy through a green glowing chamber that has a big leak of water seeping in from the bay. The boy is leading them to a nearby access point. Doggett and Bianco cross the chamber into another tunnel, but the trains are rolling and one is coming right toward Doggett. In moments it will splash through the seawater that contains the medusa, probably contaminating everyone on the train. Doggett has an inspiration – he uses his gun to short out the rail that carries the electric power for the trains, feeding a high electrical charge into the puddles of seawater. The electrical discharge kills the medusa, including wiping it off Doggett's and Bianco's skin.

At the hospital, Scully informs Doggett that his body is rid of the organism. He can be discharged. The boy is with social services. The others who are injured will be worked on by plastic surgeons. Doggett wants to charge the transit supervisor with reckless endangerment, but the organism can no longer be found. There is no evidence and the officials can easily claim that they were just doing their job by keeping the trains running. Doggett is frustrated, but Scully has experience with this kind of unsatisfactory ending to a case. Doggett recognizes Scully for figuring it out. He was just the yes and ears.

The February date stamp is taken from the reference to the "Survivor II" television series and from Doggett's reference to it being the middle of winter.

Per Manum.  A woman, Kath, is in the hospital, about to give birth and the doctor orders an emergency C-Section because the baby's heart rate is high. When her husband, later identified as Duffy Haskell, leaves the room to scrub, a nurse locks the door behind him. The mother is distraught and is knocked out with drugs. When the baby is born, it appears to be alien.

When Scully arrives at the office, Haskell is there, talking to Doggett. He is with the Ohio Mutual UFO Network and he communicated with Mulder eight years ago, claiming that his wife was a multiple abductee. He says she is dead, killed by doctors after giving birth to an alien baby. He has an ultrasound showing that the baby was not normal, and his wife wasn't supposed to be able to have babies. When Haskell leaves, Doggett points out that his wife's story is very similar to Scully's, which Doggett has read in the X-Files, except for the baby, but Scully tells Doggett that her personal files are private. In the elevator, Scully has a flashback to when she first told Mulder that she could not have children. He, in turn, told her about finding her ova in the research facility run by the Kurt Crawford clone. He immediately took the ova sample to a specialist, who said that they were not viable. Doggett interrupts her reverie and she tells him that there is nothing to do on the Haskell case.

Scully goes to Zeus Genetics in Germantown, MD. Nobody greets her, so she walks down a hall and hears voices – a man calming several disturbed women. Scully ducks into a room to hide and finds dozens of deformed fetuses in storage bottles. The doctor discovers her and she lies, claiming to be with a friend, then she rushes home to call her doctor, Dr. James Parenti. He agrees to meet with her, and viewers see that he is in the room with the deformed fetuses, unwrapping the body of an alien baby. Scully has another flashback to her conversation with Parenti when he told her that he and his colleagues believed that there was a chance that under their care she could become pregnant, but, of course, she needed a father. She said she had someone in mind, but had to figure out how to ask him. The flashback over, she meets with Parenti who says her ultrasound looks fine. He encourages her to tell the FBI about her pregnancy.

When Scully returns to the office, Doggett has received a call from Parenti's office about a sonogram Scully left there. He thinks she is investigating the Haskell case, since the Haskells had consulted Parenti in connection to their pregnancy. Haskell is called back in to the FBI to be questioned in Skinner's office. He has a history of making threats, in the letters to Mulder and to the Haskell's current doctor, Dr. Lev. He tells a convincing story about what happened to his wife, but Doggett says there is no record that they were ever married. When Haskell leaves, he telephones Dr. Lev and it is clear that they are conspiring together. When Scully returns home that evening we see a flashback to Mulder visiting her apartment. She had earlier asked him to be the father of her child, and he gives her his answer – yes. He is complimented, but doesn't want this to come between them in any way. He will talk to the doctor about the donor procedure. As the flashback ends, Mary Hendershot knocks on Scully's door. She was at Zeus Genetics earlier, and says that both her baby and Scully's are in danger.

Doggett drives his pickup up to an all-night restaurant, where he meets Skinner and Scully. Skinner tells Doggett that Scully has requested a leave of absence, but they don't reveal why. He is unhappy that they are not being candid with him, but Scully promises that she is not putting Doggett at risk. He sees her get into her car, where Mary Hendershot is waiting. Doggett doesn't know who Mary is, but it adds to the mystery he is trying to figure out. Scully takes Mary to Walden-Freedman Army Hospital, where they have an expert obstetrics team. She explains the suspicion that the baby may not be human and the team prepares to induce labor in Mary. Meanwhile, Dr. Miryum, a woman doctor, takes Scully into another examining room and does another ultrasound that looks completely normal. Joe Farah, an FBI agent friend of Doggett's, reports that Haskell's fingerprints match the records of a Marine named Haskell who died in 1970. David Haskell was buried in a Virginia cemetary in a Marine honor goard ceremony. Doggett talks to another friend, Knowle Rorer, who is apparently part of an intelligence agency. Rorer agrees to look into it and see if Haskell is a "spook," i.e. an intelligence agent. If he his, then his visit to the X-Files office had hidden agendas.

Doggett confronts Skinner, telling him that Haskell was a setup to get Scully to go wherever she went. Under pressure, Skinner admits the name of the Army research facility and Doggett rushes off. After Scully's tests, she is left alone to rest. She notices a VHS videotape in playback mode. Removing the tape, she sees that the label has another woman's name on it, Nancy Boxwell, with the date 11/23/00. Scully suspects that she has been duped. She rushes to get Mary and escape the Army facility. As they slip out into a parking garage, Rorer is there with a team of commandoes. He says he is a friend of Doggett's and hustles the two women into a suburban. As they drive away, military police chase them, but the suburban eludes them. Mary goes into labor and Scully demands that the vehicle stop. When they stop, the commando team members prevent Scully from attending Mary, injecting Scully with a drug that causes her to pass out.

Scully wakes up in a hospital room and finds Doggett sitting near her. He reports that both she and the baby are fine. Mary is also fine, with a healthy son. Scully believes that the boy was substituted for Mary's alien child, but there is no proof. Everyone says Scully overreacted. For example, they said that the videotape was of her sonogram, just recorded on an old tape. Scully is convinced that she and Doggett were used to get Mary's baby, and now they are also being used to cover it up. Why didn't she tell Doggett about her baby? She was afraid that "they" would use it to take her off the X- Files, and she would never find Mulder. Doggett repeats his pledge to help her find Mulder.

The episode ends with another flashback. Scully returns home to find Mulder waiting for her. The artificial insemination did not work and Scully will not have a baby. She feels it was her last chance, but Mulder hugs her and advises, "Never give up on a miracle."

(Note: Dating of the flashbacks is difficult. A reference in the episode script, not seen on the air, indicates that all flashbacks took place about a year earlier. For several reasons, this dating seems unlikely. Mulder acquired Scully's Ova in Momento Mori in February 1997. The first flashback appeared to have happened somewhat after Scully was cured from cancer, which was in Redux II, set in October 1997. There was no reference in this episode to Scully's child Emily, but it was in Christmas Carol, set December 21, 1997, that Scully told her mother that she can't have children. She may have learned she could not have children sometime during her cancer tests. So the first flashback of this episode could have been as early as late 1997. At Christmas 1997 Scully learns about Emily, and shortly thereafter Bill Scully and his wife have the baby that they have been trying to have for years. One could imply that Bill and his wife employed the services of a fertility and/or genetic clinic. In spite of the reference in the script, this timeline concludes that these two things likely inspired Scully to consult a specialist, leading to Dr. Parenti's claim that there was a chance of Scully having a child.)

This Is Not Happening.  Near Helena, Montana, a UFO zooms over a deserted rural area. A young man in a car is pursuing, taking photographs with one hand and dictating into a pocket recorder as he goes. It is Richie, who Mulder and Scully met in Bellefleur, OR, in the episode Requiem. The UFO hovers and Richie stops his car and gets out. He runs to the top of a hill, saying "This is not happening" to himself, and finds that the UFO has disappeared, but he sees someone walking nearby. Running after the man, Richie trips and finds a body on the ground.

Scully arrives at the X-Files office -- Doggett has called her in and takes her to Skinner's office. Teresa Hoese, formerly Nemmen, has been found. She was abducted just before Mulder and is now in a Montana hospital, just hanging on to life. Scully, Doggett and Skinner fly to Helena and rush to the hospital. The doctor says she has been severely mistreated. It is as if someone was experimenting on her. In addition to many other injuries, there are marks on her face as if the skin had been pierced and stretched. Police deliver their report to Doggett, after which the three FBI agents go to see Richie. He is in Montana looking for his friend, Gary, who was also abducted. Internet chat rooms have told him that there has been a lot of UFO activity nearby over the last couple of weeks. He claims to have seen someone with Teresa and police evidence also found footprints -- of Nikes. Doggett pressures Richie, asking if he thinks aliens wear Nikes. Richie responds that it it wasn't an alien, what about his spaceship? Doggett is disgusted. Scully sees it as their first break in the search for Mulder. Doggett tells Scully that he thinks she is also afraid to find Mulder, because of what might have happened to him.

Scully wakes from a bad dream about Mulder being experimented on. She goes to Skinner's room and they talk outside the motel. Scully relates a conversation with Mulder about starlight and about how the light we see may be millions of years old. Mulder thought that souls dwell in starlight and she hopes he's right. Skinner says it sounds like she is trying to prepare herself, but encourages her to stop -- Mulder may be fine. Jeremiah Smith, first seen in the episode Talitha Cumi, enters the hospital and morphs to look like Teresa's doctor. He tells a nurse to prepare Teresa to be transferred to another facility. He is wearing Nikes. Scully's phone wakes her up with the news that Teresa is gone and the doctor denies having transferred her.

Skinner and Scully drive up to the open field where Teresa was found. Doggett has called them to meet him there. He introduces Monica Reyes, an FBI agent from the New Orleans office who specializes in ritualistic crime. Doggett asked her to help with the case. She suspects that the abductions may be the work of a UFO cult, similar to Heaven's Gate, an opinion which rubs Scully the wrong way. Doggett follows and tells Scully that if she is going to contend that there is an alien bounty hunter involved, they have to part company. "Enjoy your new company," Scully says.

A man later identified as Absalom enters a rustic rural building. Jeremiah is in the building with Teresa. He is using the alien power to heal wounds on her. Absalom cries with joy while Jeremiah is performing the healing. They were almost too late, he observes. Scully finds Reyes at the hospital, looking at Teresa's x-rays. She says she is looking for evidence of implants. Scully doesn't understand. Reyes says she still believes that this is the work of a cult, but that she doesn't disbelieve the reports of alien abductions, and implants are often reported in such cases. She has worked on many cases of satanic ritualistic crimes, but never found direct evidence is Satan. ("We should talk," quips Scully.) Reyes believes that there are energies in the universe that she is sensitive to. She can sense Scully's fear. Later, Reyes is driving down a rural highway, sees a UFO and follows it. It has left another person behind. Jeremiah and Absalom are loading the body into a pickup truck when Reyes runs over a nearby hill, calling that she is a federal agent. The two men drive off before she can approach them. In the grass nearby Reyes finds a second body -- it is Richie's friend, Gary.

Scully does an autopsy on Gary. He has all of the same kinds of injuries Teresa did. Scully is more scared than ever for Mulder. Doggett and Reyes talk in the hall. When they worked together before, she helped during a three-day search for Doggett's son. She knows that Scully fears finding what Reyes and Doggett did find, i.e. Doggett's dead son. She understands that this is why Doggett is so determined to find Mulder. Reyes recognized Absalom in the field. He was a doomsday cultist who believed that an alien invasion would begin at the start of the Millennium. When that didn't happen, he got involved in credit card fraud, and other activities. Reyes also saw the license number of the pickup and traced it to a place about an hour drive away. Absalom's people are eating outdoors, around a campfire. Jeremiah comes up and says "they are coming" and "you can't let them find him." The compound is soon raided by law enforcement, including Scully, Doggett, Skinner and Reyes. There are dozens of people there, many sleeping in rough dormitory buildings. In one, Scully finds Teresa, alive and well. They question Absalom who is evasive. He now thinks that the alien invasion really did begin with the new millennium, but just not the way he expected. There are video cameras all over the compound, which he claims are to give the abductees a feeling of safety -- so they can see if the aliens return for them. Scully shows him a picture of Mulder, but Absalom shakes his head, no. In her motel room, Scully sees a vision of Mulder standing before her, but when she looks away for a moment, he is no longer there.

Reyes has reviewed the tapes and shows scenes to the others. On one, Scully recognizes Jeremiah, who she recalls Mulder believed had the power to heal. They see him morph on the video tape, changing to look like Doggett, although Doggett was never in that building. The agents return to the compound, where riot troops are still in control. Scully asks for Jeremiah. Picking out one likely suspect from a crowd, she questions him privately. He morphs and really is Jeremiah. He says that he saves abductees and he was trying to help Mulder, too. Skinner comes in. "You'd better come with us," he says. They have found Mulder, wrapped in a blanket, on the ground a distance away from the compound.

Scully rushes up, frantic to help him, but Doggett holds her back, saying that it is too late. Knowing that Jeremiah has the power to heal, she turns and runs through the dark back to the compound, but finds a UFO hovering over the main building, a light beaming down into it. She enters the shaking building; there are many of the abductees still inside. When the light goes out, Scully discovers that Jeremiah is gone. She sinks to her knees, crying, and moaning, "this is not happening." To be continued in April.

Deadalive. A graveside service is held for Fox Mulder in Raleigh, North Carolina. Doggett, the Gunmen, Skinner, and Maggie and Dana Scully are among those gathered. The pastor recites the Bible verse, "Whosoever believeth in me shall never die." Scully murmurs to Skinner how everyone else on Mulder's family is now gone, but the truth he worked so hard to find was never truly revealed to him. She can't believe she is really standing there. Scully crumbles a handful of dirt into the grave.

Three months later...Doggett and Skinner meet with Kersh. He is commending them, citing their efforts in the recovery of Mulder. Kersh has asked Skinner to also write a letter transferring Doggett off the X-Files and Doggett is being considered for promotion. Doggett thanks Kersh, but says he'd like to give the transfer some thought. In The X-Files office, Doggett and Scully talk. Her pregnancy is showing. Skinner told Scully about the meeting the Kersh. Scully tries to convince Doggett that it would be crazy to stay. He counters that in six weeks, Scully goes on maternity leave. If Doggett is transferred out, the X-Files office door will be locked, maybe forever. Doggett still has lots of questions about the Mulder disappearance and considers it an open case. Scully tells him to get out when he can or he may never get out.

On a fishing trawler in a storm 50 miles off Cape Fear, North Carolina, the crew finds a human body in their nets. Later, at the morgue, the medical examiner begins the autopsy but he body, which has clearly long been in the water, begins to move. Doggett gets a call at home, from Skinner. The body found in the ocean is Billy Miles and he is alive, in Wilmington, NC. Skinner and Doggett drive to the cemetery where Mulder is buried. Skinner is determined to open Mulder's grave but Doggett thinks it's crazy. Skinner feels that if Billy appeared to be dead but is now alive, Mulder may also really be alive, even after three months. Skinner has the casket taken to the same medical examiner who helped revive Billy. Although a local coroner attempts to intervene, they open the casket and find Mulder, his body showing signs of decay.

Scully rushes up to Skinner at the US Naval Hospital at Anapolis, MD. She demands to know if what she has heard is true. Mulder is alive, clinically, but his body and brain are all in a state of decomposition. Doggett urges her not to see Mulder, but she does, entering the room alone. She feels his chest to feel him breathe, and puts her head to his chest, crying. Back at FBI headquarters, Doggett is called into Kersh's office at night. Kersh has been in that office for six months and hasn't yet seen a sunrise from it. Kersh got a call about Mulder - he wants Doggett to drop the investigation. It's bad for the FBI. At the hospital, Scully looks in on Billy Miles, who has a brief convulsion while she is there. Scully has to explain to a nurse - she was just looking for an indication that Billy might be getting better, but she thinks the equipment may have malfunctioned, because for a moment there appeared to be two heartbeats.

At the FBI, Skinner isn't well. He staggers while walking down a hall, holding his chest. It is certainly the nanobots Alex Krycek implanted in Skinner's system months earlier. Making his way to an elevator, he finds Krycek. Skinner tells him to go to hell, but Krycek sends him another attack and Skinner returns to ask what Krycek wants. They go to the X-Files office. Krycek wants to give Skinner a chance to save Mulder's life but Skinner isn't sure it can be saved. Krycek tells Skinner that he has a vaccine developed by Mulder's father to fight the alien virus.

In the hospital, Billy regains consciousness, his body still decayed from weeks in the water. He gets out of bed and showers. The dead skin washes off his body. Doggett comes to Mulder's room. Scully is sitting there, holding Mulder's hand. Doggett has concerns about Scully's well being. Scully says that after her initial reaction to Doggett, he changed her opinion about him. She is thankful to know about him, and thankful for his concern, but that he was wrong to feel that the grave should not be opened. This is not because of her personal feelings, but because he is assigned to The X-Files. The truth about what caused this is what matters. A nurse enters and asks Scully to come - it is Billy Miles, standing in the hallway, naked and disoriented.

Billy's body looks healthy. He doesn't remember much when Scully gently questions him. He remembers the water and being on the spacecraft. They took so many people this time, but now he understands, he says. "They're here to save us." Doggett walks off and Scully follows. She accuses that he doesn't believe the evidence of his eyes. He says he isn't ready to accept a load of crap but Scully says he's just bull-headed. He asks if Scully believes the story about aliens coming to save the world, a question she doesn't answer. Later, Scully and Skinner talk. He came down after hearing about Billy. Scully reports that there isn't a piece of medical data on Billy that isn't 100% normal. It doesn't make sense, but it's like Billy literally became a new person. Skinner asks if it could be due to an alien influence, such as a virus. Scully demands to know what Skinner knows. He says there may be a vaccine, but it doesn't come without a price. At a corrections facility in Perkey, West Virginia, Doggett talks with Absalom. Doggett wants to know about the people he finds left for dead. Absalom quotes scripture but Doggett wants to know how he healed the people.

Skinner goes to Mulder's room and finds Krycek there. Krycek says to get the vaccine, Skinner will have to make sure Scully's pregnancy doesn't come to term. Skinner is shocked and refuses. Krycek says we all have lives in our hands - the question is who is willing to sacrifice. Doggett returns and sees Krycek, making him suspicious. Doggett talks with Scully, who tells him that she believes that Mulder is infected by a virus that keeps him just alive enough to transform him into an alien. Absalom also told Doggett that the abductees, if not cured, would be resurrected as aliens as part of the plot to take over the world. The double heartbeat Scully heard in Billy maybe be evidence for this. Scully is on her way to a surgical bay - Mulder's body has to be stabilized in order to administer the vaccine she has asked Skinner to get her. Doggett searches out Skinner, who is in Mulder's room disconnecting Mulder from the equipment, apparently an attempt to kill Mulder. Skinner couldn't kill Scully's baby in order to get the vaccine. Doggett wants to know where Krycek is and finds him in a car in the parking garage. Krycek tries to run Doggett down and Doggett grabs him through the car window as the car careens through the garage, but Doggett is finally thrown free. Krycek, however, stops, backs up and gets out of the car, holding up the vial containing the vaccine. As Doggett approaches him, Krycek drops the vial, allowing it to break on the floor, then drives off before Doggett can get to him

Doggett storms back into the hospital. He doesn't have the vaccine. Doggett tells Skinner he was right - Krycek wasn't to be trusted. Scully is in the operating room with Mulder when Doggett enters. Scully has realized that by keeping Mulder on life support they were helping the virus incubate. When Skinner took him off the equipment, Mulder's temperature dropped but his vital signs were unchanged. Maybe they can give him courses of antiviral drugs to help him. Doggett is called to Kersh's office again. It's going to be awful crowded down in that X-Files office, Kersh says, meaning that the promotion is no longer available to Doggett.

At the hospital, Mulder wakes up. Seeing Scully holding his hand and crying tears of joy, he jokingly asks "Who are you?". Then he asks, "Anybody miss me?" Doggett looks in, but when he sees what is happening he withdraws.

Three Words.   A man, later identified as Howard Salt, walks along the iron fence along the street outside the White House. He puts on gloves and climbs the fence, running toward the building. Secret Service agents intercept him as he calls out "He needs to know," and "Aliens are taking over the United States, he needs to know." Salt pulls a gun out of his belt, and as the agents wrestle for control of the arm, the gun fires into Salt's abdomen. As Salt passes out, he hands a CD-ROM to an agent, asking him to give it to the President. On the CD-ROM is written, "Fight the Future."

Mulder is in his hospital room, gently touching the wounds on his face and remembering what was done to him during his abduction. Scully and a doctor enter. They have important news. In addition to Mulder's incredible recovery, Mulder's terminal disease is no longer detectible. The virus is gone, after the treatment with antiviral drugs and blood transfusions. The scars on his face and body are repairing themselves. He is in perfect health. Mulder says he feels like Austin Powers. Later, Scully takes Mulder home to his apartment. He looks around and notices that one of his fish is missing. Scully tells Mulder he can't understand what it was like -- learning of his abduction, searching for him, finding him dead and now having him back. Her prayers have been answered. Mulder says that her pregnancy is also an answer to her prayers, and he is happy for her. He, however, has no idea where he fits in now. He is having trouble processing what has happened to him.

At the federal prison in Perkey, WV, a trustee is circulating library books to prisoners in a common area. He has the new Harry Potter book. He hands Absalom a book, "The Coming Apocalypse." Inside the front cover is a newspaper clipping about a census worker shot on the White House lawn. Deputy Director Kersh is watching a TV report about the census worker when Doggett and Skinner enter his office. People are so rarely what they seem, comments Kersh. Scully has submitted an application to reinstate Mulder on The X-Files. Kersh intends to deny the application. The success rate on the X-Files since Doggett was assigned is much higher than during the time when Scully and Mulder worked together, he says. The FBI is no place for a personal crusade, Kersh says, and directs Doggett to tell Mulder that he will not be reinstated. Kersh says the alternative is closing the X-Files completely.

Skinner and Scully actually tell Mulder about Kersh's decision. Mulder thinks it's something that was set up eight years earlier. For the first time, Mulder is told that Scully has had a partner for the last several months. Doggett doesn't know much about the paranormal, but Scully says he is above reproach and is also being maneuvered. Mulder intends to go back to work anyway. In Bassett County, WV, a prison work crew, including Absalom, is working on a road. In the dirt, Absalom finds a board with a nail sticking out and slips it into the sleeve of his orange jumpsuit. As the prisoners are loaded into a van, he uses the board to strike a guard and runs. He is pursued, but he eludes the guards by running in front of a passing train, which blocks pursuit.

Later, Doggett returns home to find Absalom waiting for him. Absalom grabs Doggett's gun and holds it on him. Doggett is ordered to put his hands behind him and lean forward so Absalom can check the back of his neck. He has to make sure that Doggett is still Doggett, he says. Doggett is shown the newspaper clipping. Absalom claims "they" killed Salt for what he knew, just as Absalom's life is threatened. He vows to show Doggett after which Doggett will spread the word. The invasion has begun. They are already here. As Absalom utters Biblical phrases, the phone rings but Doggett is not allowed to answer. It is Scully calling. She is with Skinner in a briefing about Absalom's escape. The words "Fight the Future" were found on the wall of Absalom's cell. The agents in the room are skeptical about reports that Absalom made claims about alien abduction, healing and alien invasion. Skinner stresses that while the claims are not substantiated, neither have they been refuted. The evidence of torture was real. Skinner tells Scully that this is obviously an X-File and he wants Doggett to be running it. Scully answers that she is "all over it." As they talk, Scully's cell phone pager beeps with a message from Mulder, "Where is everybody, come on down."

They find Mulder in his office, feet up on his desk. By being there, he could be endangering the X-Files, but he brushes off such warnings. Mulder already knows about Absalom and has noticed that Salt is seen in a photograph taken of people at Absalom's compound. Mulder doesn't know any more than that, but has a big hunch. Salt, he says, was a multiple abductee, was trying to get word to the President and was killed for what he knew. Scully and Mulder visit the FBI evidence room. Mulder locates Howard Salt's personal effects, including Salt's laptop. The entire hard drive is taken up with a ten gigabyte encrypted file. He removes the hard drive and they leave the evidence room.

Absalom and Doggett arrive at the Federal Statistics Center in Crystal City, VA. Absalom has taped a gun to Doggett's back so that it would fire into Doggett's skull. Absalom has his hand on the gun. Doggett's FBI credentials get them through the guard post, but a hidden x-ray locates the gun. Absalom wants access to the place they compile the data from the current census. He thinks there's proof in the census data that the aliens are already among us. As the two are about to enter the computer room, guards appear with guns. Doggett calls to them to back off and lower their weapons, but one guard shoots Absalom through the forehead, killing him instantly.

Doggett is in Skinner's office. Skinner asks about Absalom's claim that the census records contain proof. Mulder enters and Skinner has to hold him back from roughing up Doggett. Mulder thinks Doggett is busy burying the truth. He got Absalom killed for what he knew. Later, Frohike greets Mulder at the door to Scully's apartment. It's not fair, Frohike says, that Mulder has been dead for six months and still looks better than Frohike. Byers and Langly are also happy to see him, although Langly implies that Mulder may have been involved in a "certain blessed event." The Gunmen were able to partially decrypt the file on Salt's hard drive. The data was downloaded from the Federal Statistics Center (FSC) the day Salt died. Fifteen minutes after Salt was shot, firewalls went up on the databanks of the FSC. Mulder thinks that means he's right and that they would kill to protect what is in the files. Unless Mulder can find a password, there is no way to get into the data. What is on the hard drive is apparently just a directory structure. Scully has gotten the Gunmen to try to convince Mulder to let this one go, but Mulder remarks that this is America - just because you get more votes doesn't mean you win.

Doggett approaches his friend, Rorer as Rorer is jogging. rorer compliments Doggett for dodging a bullet. Doggett wants to know if he is being used. Rorer can't tell him that, but he can tell him three words. Later, Doggett stops Scully outside her apartment building. He can't go upstairs because Mulder doesn't trust him. Doggett tells her that Salt had a computer diskette that he was trying to get to the President, according to Doggett's source. The password for the data is "fight the future." Scully goes inside, where Mulder is waiting. She hesitates, but tells him of Doggett's information.

Someone knocks on Doggett's door - it is Skinner. Scully called, beside herself. Mulder somehow got access to a password to a federal database filled with names of people of a certain genetic profile being tracked using the US Census. Doggett confesses that he gave Scully the password, but now he doesn't know which side he is helping. He declined to tell Skinner more. At the FSC, Scully is parked outside in a car when Doggett knocks on her window. Mulder wouldn't listen to her. Doggett tells her to leave. She thinks she can't do that to Mulder, but Doggett tells her to do it for herself. He thinks he may have set Mulder up. Doggett runs into the FSC. Mulder and the Gunmen are inside, working to penetrate the FSC security.

With the Gunmen's help, Mulder gets inside without the security guards noticing. Doggett finds the guard's office empty. Mulder arrives at the computer room and the Gunmen remotely open the locks. He uses a workstation to access the data and prepares to e-mail the data. Doggett pounds on the door, which is now locked again, calling that Mulder's life is in danger and to get out of the room. Mulder ignores him. Doggett fires his gun through the glass door, jumps through the door and again warns Mulder of the danger. Mulder thinks Doggett is trying to protect the data, which Mulder says proves that aliens are targeting certain people based on their genetic profile for abduction and replacement by alien facsimiles. He begins to send a copy to the Washington Post. Guards drive up in military vehicles. Scully sees them arrive and uses her cell phone to warn the Gunmen that Mulder has to get out. Mulder again thinks Doggett has set him up, but Doggett says they've both been set up and they will both be killed. Langly radios to Mulder that the data has been trapped and can't be uploaded for transmission. Byers has a long shot idea for how they can get out. The guards storm into the computer room and Doggett and Mulder are not there. They are hiding above the suspended ceiling.

Rorer is jogging again. As he stops at a drinking fountain, Doggett approaches him. Why shouldn't Doggett expose Rorer? Skinner is walking toward them across the park. If Rorer walks, Skinner will see to it that Rorer's name goes in lights. Rorer asks if Doggett exposes him, where will he get his answers? Doggett is standing on the tip of an iceberg, he says. It's not about Mulder, Rorer says, it's about the truth. Doggett has it all right in front of him in the X-Files. Rorer says he is just trying to point Doggett in the right direction. As Doggett walks away, we see that Rorer has a lump on the back of his neck.

Empedocles. In New Orleans, an executive and his assistant have to fire an employee - you've done a good job here but the economy is the result. As the employee, Jeb Duke, leaves the building, he witnesses a police chase and the car being chased slams into another vehicle, exploding. As Jeb stares, it appears to him that the driver of the car, burning on fire, gets out of the car and walks past Jeb. Jeb's eyes blaze for a moment, and then Jeb runs off. Later, he returns to the office and shoots his former boss and the assistant.

Monica Reyes arrives at the crime scene. The officer in charge has reason to believe that the killings may be satanic. Jeb had some artwork at his desk that appeared to be satanic, but Reyes recognizes them as artwork used by a popular recording artist. Reyes doesn't think there is a satanic angle, until she sees the arm of one body under a sheet and has a vision of it turning to ashes. Mulder calls on Scully at her apartment. She was waiting for the pizza man and Mulder jokes, implying that Scully is having an affair with the pizza man. He sneaks a wrapped present into her house. She finds the package - he says it is an old family keepsake he came across. The pizza man comes to the door, but as Scully begins to open the package, she has severe abdominal pains. Mulder arrives at the hospital in the ambulance with Scully. Doggett soon shows up, having received the news about Scully. While they wait, Reyes phones Mulder asking for help on her case. He refers her to The X-Files unit, but she says she can't call Doggett because it involves him. He says to call when she gets to Washington. Scully, it turns out, is not in immediate danger and the doctors are going to run some tests.

Jeb is at a motel. He picks up his gun and holds it to his head, but it glows red-hot and burns his hand, and he cannot kill himself. His scratches his face, and he seems to be glowing with fire inside his body. At FBI headquarters, Reyes is reviewing boxed files in a storeroom when Mulder enters. She reminds him that she was there when they found him in the woods. Her case involves the death of Doggett's son, Luke, when Doggett was with the New York City Police Department. Reyes was the lead investigator for the FBI and worked closely with Doggett on the case. The killer was never found. She doesn't want to put him through this again, unless she knows whether what she saw means anything. When they found Luke, Reyes had a vision, as if for a moment the body was changed to ashes. Doggett saw it too, although he later tried to convince himself that he didn't. Now she has seen it again on a seemingly unrelated case. There has to be a reason. Doggett is still at the hospital, checking in on Scully, who is sleeping. He has a flashback to the discovery of his son in a wooded field. A nurse interrupts the flashback, kicking him out of the room.

Mulder is in the basement of the FBI office when Doggett accosts violently him for sneaking through files relating to Doggett's personal life, i.e. his son's death, but Reyes comes down the hall and intervenes and tells Doggett about her vision. Bob Harvey was a suspect in the death of Luke, but was not charged. Harvey was killed in the car crash that Jeb witnessed. Doggett is adamant that there is no connection and he wants them to leave it alone. Reyes is still sure that there is some connection. She calls on Jeb's sister, Katha Duke, who lives with her young daughter. Jeb lived in the house with them until he moved south. She doesn't recognize the name Bob Harvey. While Reyes is there, Jeb calls, claiming that it was somebody else who killed those people. Jeb is calling from a rural phone booth and a woman who says she has a flat tire stops him. Doggett visits Scully in her hospital room again. She is still feeling the effects of sedatives. He asks her about Mulder and how she came to believe in the paranormal. What changed her mind was realizing that she was afraid to believe. Doggett has another flashback to the discovery of his son and cuts the conversation with Scully short. Reyes finds Mulder in the X-Files office, even though it is not his office anymore - just habit, he says. He has several files similar to the vision Reyes saw, but in the cases the visions seem random and don't have much relevance to the cases. Mulder thinks Harvey's death was a coincidence, but Reyes disagrees. Reyes accuses Mulder of not having an open mind.

Jeb walks through the countryside and arrives at the minivan with the flat tire. In the window he sees the reflection of himself with flames behind him. He gets in the car, now with its tire replaced, and drives off. Later, police are at the scene later when Doggett drives up. Mulder is there and has summoned Doggett. The woman's body has been found a short ways off the road and Reyes thinks the killer is Jeb. When Doggett looks at the body, he says he does not see a vision of it turning to ashes. Reyes suggests that he is afraid to see it. She can't blind herself to the connections. What if this is a threat of evil, connecting through time and men and opportunity back to Doggett. Doggett just can't bring himself to see it. Later, Mulder calls on Scully. She had a problem with her placenta and needs to be monitored, but she should be fine. She asks where Mulder has been and he tells her about it. She tells Mulder that Doggett is worth the effort to help. Jeb's sister arrives home to find Jeb there. He swears that he didn't do what they say. Katha sees blood on his face and he claims he doesn't know how it got there. He repeats that he is not the killer and that he needs help.

Doggett is working on the case when Reyes enters his office. She says he shouldn't be phone canvassing but he insists that proper police work will find Jeb. She wants him to be honest about what he saw and his feelings. She asks him what he's scared of. He replies that he's got to believe that he did everything he could to find his son and to save him. He is afraid that he let his son down, and if these other possibilities are real, then it represents something else he could have done to save Luke. The phone rings - it is Jeb's sister. Doggett and Reyes rush off. Jeb is reading to his young niece. Katha wants him to talk to Reyes, but Jeb reacts strongly, grabbing his niece. Jeb and Doggett soon are in a confrontation, Jeb's gun on Doggett. Reyes shoots Jeb to save Doggett and the niece. At the emergency room, Doggett and Reyes come in with the ambulance. Reyes thinks maybe saving the little girl is why this all happened. She sends Doggett home, but instead he goes to Scully's room in the same hospital and has yet another flashback. He sees Luke dead on the ground and sees the ashes. Mulder steps in and wants to talk to Doggett. When Mulder first worked for the violent crimes unit, he saw the worst of humanity and began to think of evil as a disease. Most people can stifle that momentary urge to kill, but some people experience tragedy or loss that overwhelms that urge. Does that mean that Jeb is effectively evil, Doggett asks? Mulder says Doggett may never know for sure.

Katha is with Jeb in Intensive Care when he goes into convulsions. His heart stops and doctors can't save him but something passes from Jeb to Katha, and her eyes glow momentarily. Reyes enters and Katha attacks her. Doggett rushes in and subdues the sister, knocking her unconscious. He tells Reyes "it's over now" and she says "it's never over." Scully is back home and Mulder is visiting. He brought pizza of his own. She finally gets the present opened and finds a child's rag doll, which Scully with cherish. The other gift he gave her is courage, a gift she will try to pass on. At the hospital, Doggett is keeping watch on Katha, who still appears to be unconscious.

Vienen. On an oil-drilling platform at sea, the workers are in a bar/lounge/restaurant area. The TV goes out and the drill rig boss, Bo Taylor, hits the TV, causing it to work again. One of the workers, Simon do le Cruz, goes off by himself to a shop where another man is repairing a radio. Simon carries a knife from the kitchen. In the lounge, the TV goes out again and pounding on it doesn't fix it. Taylor goes to find the rig's communications officer. He finds Simon battering the radio. The Communications man is dead. Simon is there, and is clearly frightened. Taylor's body begins to glow and Simon screams.

At FBI Headquarters, Doggett finds the door to the X-Files office locked. He unlocks it and enters to find Mulder looking through the file drawers, researching the recent death of an oil worker. Doggett understands that Mulder is interested, but points out that he is not assigned to The X-Files. Simon's body washed ashore with serious burns. The oilrig's communications officer is also reported as missing. The medical examiner said the burns are consistent with radiation burns. Doggett is well aware of the files on the Black Oil that is radioactive and can allegedly take over human bodies, but he is not convinced about it. The phone rings - it is Scully in Kersh's office. There is an oil executive there who says somebody in the X-Files office contacted him. It was Mulder, working unofficially.

Mr. Ortega is waiting in Kersh's office, and Kersh is unhappy that Mulder has been investigating the case. They have a sensitive situation - the company has located what appears to be a huge new oil reserve, which may spread into Mexican territory. In order to diffuse the possible international situation, Kersh reluctantly agrees to have the case investigated. He sends Doggett, who arrives at the platform by helicopter, 150 miles out to sea. A new communications specialist also arrives. Doggett discovers that Mulder is already there. Taylor tells the two agents that Simon went crazy and tried to blow up the rig, causing a gas valve to explode, also killing the communications chief. When Mulder and Doggett aren't looking, viewers see that Taylor has black oil in his eyes. Later, in private, Mulder and Doggett argue. Mulder isn't supposed to be there. Both agree that Taylor is lying.

Scully does an autopsy on Simon's body. In his brain, she found evidence of the alien virus, but it is dead. What killed it? Scully demands an evacuation of the oilrig, in case the virus is loose. The new communications specialist is working on the radio, which is still nonfunctional, when Taylor enters. There is some sort of high frequency interference being received over a large range of channels. Taylor knocks the man out and black oil drips out of Taylor's eyes and mouth, infecting the communications man. Later, Scully uses the now working radio to send a message to the oilrig and is surprised to learn that Mulder is there. He suggests that Kersh doesn't need to know that he is there. She confirms that the virus was in the body but is dead. Could the radiation have killed it? It seems unlikely, since the black oil is radioactive itself. Everybody in the rig is in danger. Scully wants to evacuate the rig and quarantine the people. Mulder counters that Scully needs to find what killed the virus. Doggett overhears part of the conversation and demands from Mulder to know what is happening. Later, the news is announced to the workers that Doggett has ordered the rig has been quarantined - nobody can leave or arrive at the rig. The workers all grumble.

Mulder has reviewed the crew manifest. There is one other crewmember missing, Diego Garza. He is a deck hand and was a friend of Simon. Nobody has any idea where he might be. Scully shows Simon's body to Ortega. He says there is no evidence of any disease and if they can't give him any, he'll call in the crew and rotate a fresh crew to the platform. Mulder is looking for Diego but Doggett thinks Mulder isn't giving straight answers. Mulder claims he doesn't know what the oilrig workers are hiding. Mulder has seen how this substance can take over a man's body. It body jumps from man to man and it's not in all oil. Mulder thinks the new oil complex is already being pumped and that the oil is filled with the virus, ready to infect the planet. Maybe Diego is hiding because he knows what is going on. As they talk, an alarm goes off. It's the radio room, on fire. Mulder grabs a fire extinguisher and as Doggett runs down the hall to get another, Diego knocks him unconscious.

Kersh and Skinner visit Scully in the morgue. The body should have been well on its way back to Mexico by now. Kersh got a call from Martin Ortega about the rig being shut down. Kersh intends to order the quarantine lifted. Scully counters that communications is out so the order lifting the quarantine can't be delivered. Kersh threatens Scully and Skinner that they are running out of mistakes. As the sun sets on the platform, Mulder concludes that the fire that damaged the radio equipment was arson. Doggett wakes up to find Diego holding a knife on him. Diego pokes him to see if his blood is red. Doggett doesn't speak very good Spanish and their conversation is halting, in English and Spanish. Diego set the fire to keep the others from using the radio. "They" have to be stopped before it is too late. "They" are coming. Who? The flying ships are coming. Scully finds a large number of T-Cells in Simon's blood, cells used to fight virus. Simon may have had a genetic immunity to the virus because he is from a rare group of indigenous Mexican Indian people. Scully thinks the rest of the rig workers killed him because he was a threat. It could actually put Mulder and Doggett in danger if they did get word to them.

Doggett and Diego continue to talk. Doggett says if Diego stays there, the other workers will find him. Doggett promises to help Diego get home. Later, Doggett crawls out of the space where Diego was holding him, apparently having reached agreement with Diego. Taylor intercepts Doggett, knocking him down and beginning to drip oil, but Mulder arrives and knocks Taylor unconscious, saving Doggett. They head for the radio room and lock the door. Doggett will try to get the radio working while Mulder barricades the door. Outside, the oil workers gather can begin to break down the door.

Mulder piles furniture against the door as Doggett gets the radio working. Scully is on the other end. Scully thinks she knows why they killed Simon. The choppers are on the way to evacuate the platform, but Mulder orders that the helicopters not land. Doggett tells Scully that only three of them on the platform are uninfected. Mulder abruptly breaks the radio, and when he does, the hammering on the door stops. He had to prevent the oilrig workers from using the radio, because apparently they would use it to signal their flying ships. The oilrig workers are no longer outside the radio room. Mulder and Doggett cautiously leave the room to find out why, Doggett calling to Diego as they go. They find Diego's body, burned. They hear the chopper arrive and continue making their way up to the deck of the platform. Mulder thinks that the workers are about to blow the rig. Flames break out as the two agents run over catwalks and through equipment rooms. In one area, Taylor and his men block their way. Explosions rock the platform. Ultimately, they come to a catwalk and jump into the water as the platform explodes, to soon be rescued by a hovering helicopter.

Back at the FBI office, Doggett again finds Mulder in the office. Doggett has been called to Kersh's office. The oil company has lost the right to drill on that undersea oil complex. Mulder wants the oil to stay where it is. Mulder tells Doggett that the blame will be properly fixed - on Mulder. He is out of the FBI. Mulder is taking a fall for Doggett, for the X-Files. Doggett has seen the oil for himself. Doggett is in charge now of The X-Files now. Mulder walks out the door as the episode ends.

Alone. On a stormy night in Ellicott, NY, Gary Sacks drives up to a house and enters. An older man, his father named Arlen, is in a wheelchair in the house. They discuss whether Arlen should be in a hospital, and about how the locks have to be checked every night. Gary says his father doesn't owe "Stytes" anything. When Gary leaves the room we see that a window is open. Arlen's heart monitor begins beeping faster and faster. Gary, in the kitchen, hears the heart monitor beep flatline. Arlen's wheelchair is overturned and Arlen is missing. Some sort of reptilian creature the size of a man jumps Gary.

Scully is in the X-Files office, cleaning out Mulder's desk, looking at memorabilia from past cases. Doggett enters. She's not staying – her doctor told her to begin her maternity leave. She gives Doggett her medallion commemorating the Apollo 11 space flight. Mulder once gave it to her, symbolizing teamwork and partnership. She thanks Doggett, saying she wouldn't be here without him. They hug. Doggett wants to be sure that this pregnancy leave is just a leave, and that Scully will be coming back. She just smiles at him. Another agent enters, a young woman named Harrison. She has a murder in up-state New York to be investigated. She has been assigned to work with Doggett on The X-Files. In Ellicott, they see Arlen's body being removed. It was found in the woods near the house. Arlen was the groundskeeper of an estate. His son, Gary, is missing and is a suspect. On the frame of the open window, and on the floor, Doggett finds traces of slime. Harrison is young and enthusiastic, but clearly inexperienced. It's her first time in the field. Kersh gave her the job. Doggett says she is being used, but Harrison counters that she begged for the assignment. She was in accounting and processed Mulder and Scully's expense vouchers. She is excited to be part of this case. She knows about liver eating mutants and aliens shedding skins. More slime is found where Sack's body was found.

Mulder picks up Scully to go to the hospital. She is feeling strange about everything, especially leaving work. She feels like a deserter. Mulder senses that she is concerned about Doggett. He "watched her back," but Mulder says Doggett can take care of himself. Doggett is looking through the woods and approaches a large mansion. It appears deserted, with cloths over light fixtures and furniture. By a computer Doggett finds a book by Robert Leakey, The Sixth Extinction. Something moves down the hall and Doggett draws his gun, but it is Harrison. He hushes her and tells her to draw her gun. He sends her outside to the front door – whatever it is in the house, he will try to flush it out. She goes outside and discovers the reptilian creature on the wall above her. Doggett hears gunshots and rushes outside. Harrison is gone. Walking through the grounds, he steps in a trap door in the ground and falls in.

Other agents are searching the woods, lead by Skinner. Scully phones and asks if it the report of Doggett being missing is true. She wants to come and help, but Skinner tells her to stay put. Doggett wakes up in an underground passage. He picks up his gun and draws a flashlight. His cell phone reports no service. Mulder and Scully are at the morgue. Arlen Sacks died of heart failure after being blinded by some kind of substance. Mulder says it is venom, based on the sample Doggett and Harrison sent back. Doggett breaks through a metal gate across the passage. He finds a wine cellar, then hears a noise. The reptile jumps him, but he fires his gun and drives it off. Harrison comes into the room. Both of then had their eyes sprayed and their vision is blurry. She has also found Gary, who is comatose nearby. Doggett thinks somebody provided the trapdoor to provide meals for the reptile. Bootleggers probably built the tunnels during the depression. Mulder drives up to the search location and talks to Skinner. Police found Doggett's car parked at a convenience store some distance away and the search is being moved.. Mulder decided to do his own search in the woods. Doggett is trying to climb out of a manhole , even though his vision is blurry Mulder approaches the mansion Herman Stytes, who says he owns the property, approaches Mulder. Mulder asks if Herman has seen any dangerous animals. Mulder gives his name as Alvin Kersh. Herman says he is a biologist. Mulder thinks that the reptile is a man, using some kind of reptile venom. Mulder walks away. Doggett gets to the top of the manhole shaft, but Stytes steps on his hand, causing him to fall back.

Doggett thinks that the man is some kind of scientist. Doggett tells Harrison to stay with Gary while he looks for a way out. Harrison, however, discovers that Gary is gone. Did the thing take him? Mulder is watching the mansion when Scully calls. She says Stytes called and complained about Mulder impersonating Kersh. Scully thinks this is some sort of reptile attack. Mulder found his Apollo medallion on the grass on Stytes' estate, so he knows Doggett is nearby. The bacteria in the slime is breaking down the dissolving the body of the victims, according to lab tests. Doggett and Harrison are making their way through the tunnels. She is completely blind. Doggett catches a glimpse of the reptile and shoots as it crawls along the walls. Gary is in the same room with them, his body largely dissolved. Scully reports to Mulder that Stytes is a cryptobiologist who published a monograph last year claiming to be on the verge of creating a new species of reptile. Mulder sees something slithering around the grounds and chases it. It climbs the mansion wall and disappears. Mulder pounds on the mansion door, which is locked. The reptile is just inside, and transforms in to Stytes. Stytes opens the door. Mulder wants to know where it is. Mulder and Stytes find Doggett and Harrison in the tunnels. Doggett reports that Stytes is protecting the reptile but Harrison claims that Stytes IS the reptile. Stytes locks them in, then transforms in to the reptile and stalks them. Doggett can't see but Mulder directs him how to fire his gun to kill the reptile. When it is dead, the reptile transforms back into Stytes.

At Washington DC Memorial Hospital, Doggett is recovered, having received anti- venom treatments. Harrison is recovering, but she has decided that she will not return to the X-Files. Mulder wants to return the Apollo 11 medallion to Doggett, but Doggett wants to give it to Harrison. Mulder and Scully visit Harrison, who asks a typical fan question – when Mulder went to Antarctica to save Scully from the alien spaceship, and his snowcat ran out of gas, how did they get home. Mulder and Scully don't answer, but begin quibbling over whether it was really a spaceship, enjoying themselves.. Doggett listens at the door briefly, and walks off, alone.

Essence. The episode begins with a narration by Mulder about the miracle of life – or is it just nostalgia for something commandeered by science. How did this child come to be? Is it a miracle or a product of technology?

Scully's mother, Maggie, is helping decorate Scully's apartment for a baby shower. Lizzy Gill arrives, a baby nurse Maggie has asked to help Scully. While the shower is going on, Lizzy replaces the pills in Scully's prescription bottle. At Zeus Genetics, Dr. Lev is working late when Billy Miles enters. He's there to verify that Dr. Lev's work has been fruitful. It has, but his work is done. Billy kills Dr. Lev, dousing the body with a chemical and setting it on fire. Doggett is cleaning his gun on a Saturday morning when Mulder comes to his door. The Zeus Genetics building has burned and Mulder wants to be involved because it's the place where Scully thought they were creating alien babies.

The two visit the FBI evidence analysis facility which is sifting through the debris from Zeus. Doggett's friend, Gene, resents that it was Mulder who initiated the search. All of the Zeus staff is accounted for but Dr. Lev. Lev's co-founder of Zeus Genetics was Dr. Parenti, who was Scully's obstratician for the first two-thirds of her pregnancy. Mulder and Doggett go to question Parenti. They gain access to the office, believing that nobody is there. Parenti actually is there, meeting with a patient. In Parenti's office Doggett finds many glass containers with preserved fetuses. Parenti says they are babies with birth defects. Scully takes her perscription pills as Lizzy is about to leave. Outside, Lizzy is picked up to Duffy Haskel. She tells him that Scully trusts her and Haskel replies, "Good, we're almost at an end."

Dr. Parenti is packing the things in his office when Billy enters. When Mulder and Doggett arrive to further question Parenti, they find the doctor's head in one of the glass canisters. Mulder finds Billy in the office, who tosses Mulder through a glass panel. Doggett fires his gun at Billy's chest, but Billy keeps coming. Doggett ducks into an office, and when he looks out again, Billy has disappeared. Doggett and Mulder go to Scully's apartment, where she cleans a cut over Mulder's eyebrow. Mulder thinks Billy is an alien "human replacement." Doggett counters that Billy bled red blood when he was shot, and the X-Files show that aliens bleed green. Mulder speculates that Billy is something new. Lizzy arrives while they are talking and from another room calls Haskel to report that there is trouble – that the agents are asking all the right questions. While on the phone, Haskel is attacked by Billy.

Dogett arrives at the crime scene where Haskel's head has been found, severed from his body. Skinner and Mulder are there, too. Skinner says the building has been determined to be an illegal medical facility for the purpose of human cloning and that prenatal records indicate that Lev and Parenti were monitoring Scully's pregnancy. Skinner asks Mulder about the fatherhood of Scully's baby. Mulder has no idea and Skinner stresses that he needs answers. Mulder phones Scully, who has to leave the shower to answer. She catches Lizzy substituting more prescription pills. Scully is checked out at the hospital, and everything is fine. The replacement pills were just vitamin supplements. Skinner, Mulder and Doggett gather at Skinner's office to question Lizzy, who says that for ten years she has been a scientist working on a secret human cloning project. They were funded with government money from men who are all dead now. They were successful with a clone combining human and alien DNA. The babies only survived a couple of days, but they provided tissue and stem cells for other work, which Lizzy claims to have no knowledge of. Lizzy says Scully's child is very special – a perfect human child with no human frailties. Mulder storms out. Doggett's friend, Gene, tells Doggett that Billy has called in from Dr. Parenti's office, offering to give himself up. Doggett takes a SWAT team to Parenti's office, but Billy is not there.

Mulder arrives at Scully's apartment and tells her to pack a bag quickly because she is in danger. He is going to do everything he can to protect her baby, but he can't do that at her apartment. Doggett phones to report that Billy is not where he said he would be. The lights go out in Scully's apartment and Mulder and Scully run. As they head down the hall, Billy approaches from the other end of the hall. Scully's car is blocked in by two other cars. As Billy approaches, he is struck by another car, driven by Krycek. Although Krycek's car completely passed over Billy's body, Billy is recovering rapidly. Krycek calls out that they don't have much time and in a split second, Mulder and Scully decide to go with Krycek. They all gather again in Skinner's office. Krycek says that there are others just like Billy and that they are virtually unstoppable. They are working to end the resistance to the alien's return to the planet. Why do they want Scully's baby? They are afraid of it, because they realize that it could be greater than them. Krycek asked Skinner to kill Scully's baby (a few episodes ago) because he wanted to destroy the truth. Mulder leaps to the conclusion that this truth is that there is a higher power, a God. Krycek says that there is no hospital that is safe enough for Scully.

Doggett calls in help, including agent Monica Reyes, who is on her way to the airport in a taxi. She diverts to the FBI building. Doggett waits for her in the parking garage and phones to Skinner and Mulder to bring Scully down when he sees Reyes' taxi pull up. As Reyes drives up, however, Billy is seen in the parking garage and Doggett tells Skinner and Mulder to take Scully back up in the elevator. Billy heads up the stairs. Skinner and Mulder leave Scully with Krycek and head out to intercept Billy. Krycek gets her to the garage and Reyes drives off with Scully, slowly negotiating the curves of the parking garage. Gene stops them at the parking garage exit to the street. On the roof of the building, Skinner encounters Billy. Mulder runs up and knocks Billy over the edge of the building. Billy falls into a garbage truck, several stories below. Gene waives Reyes on and she drives off with Scully. Viewers see that Gene has a bump on the back of his neck.

Existence. Billy Miles' remains are brought into a medical examiner's lab. The body was crushed after falling into a garbage truck. In the pulverized remains, the doctor finds what appears to be a metallic vertebra. He leaves it on the counter when he leaves the room. The piece of metal spins of its own accord. Each time it spins, it multiplies itself, as if creating a new backbone - apparently Billy's body is rebuilding itself out of almost nothing.

Scully is riding in a car drives by Reyes. They are in Georgia, where they hope Billy cannot find them. Reyes is concerned that she has never delivered a baby and there will not be facilities where they are going. At FBI headquarters, Mulder and Doggett are with Skinner and Krycek in Skinner's office. Video from a surveillance camera shows Billy Miles leaving the morgue. Doggett doesn't believe it is possible. Krycek can't explain it, but says Billy is somehow a human replacement - some new kind of alien, created to aid in the repopulation of the planet. The aliens think Scully's baby is a threat to their plans. Agent Crane gives Doggett the message that Knowle Rorer wants to talk to Doggett. They meet and RorerRorerRorer tells Doggett that both Billy and Scully's baby are products of a cold war effort to create a super soldier. Scully's abduction was by the military, and the chip in the back of her neck was used to make her pregnant with the first organic version of the super soldier. RorerRorer wants to stop Billy before he can get to Scully.

Scully and Reyes arrive at Democrat Hot Springs, an abandoned community in Georgia where Doggett was born. It used to be a popular spot among the rich. Only Doggett knows where they are. It is night and the rooms are dark and dirty. They begin making plans for Scully's labor. Outside, Reyes sees some kind of bluish light in the distance. Billy shows up in the FBI building causing Krycek and Skinner to run. Skinner barely escapes Billy by jumping into an elevator and Krycek, already in the elevator, does not lift a hand to help Skinner. Skinner is seriously wounded. Mulder is with Skinner in the hospital when Doggett arrives. Doggett tells Mulder about his conversation with Rorer, making clear that Doggett doesn't trust Rorer. Mulder doesn't want Doggett to tell anyone where Scully is - not even Mulder. Doggett is wondering whether the fact that he knows where Scully is will catch up with him. Mulder points out that Rorer didn't say HOW they intend to stop Billy.

Reyes has the house cleaned up and arranged for the labor, impressing Scully. Reyes talks about needing mood music, suggesting whale songs, reminding Scully of her sister, Melissa. Reyes sees someone outside. It turns out to be a female park ranger. The ranger is skeptical of the claims that she is talking to two federal agents hiding from a very dangerous man, but she eventually gives them the benefit of the doubt and volunteers her first aid kit, and to go get further supplies. Scully asks Reyes if she is feeling any "vibrations." She says something feels "off," but she can't identify it. Reyes goes outside to get water from a pump well. The glowing blue light is still there in the distance. Billy appears out of the dark and attacks her but the park ranger, who has just returned, shoots Billy, saving Reyes. Scully comes outside to see what is happening, but feels her first contraction. Her labor is beginning.

In the FBI parking garage, Mulder and Doggett see Rorer in a car with Krycek. Doggett follows Rorer when Rorer leaves the car and Mulder watches Krycek. Doggett sees Rorer talking with Agent Crane outside Deputy Director Kersh's office. Doggett slips downstairs to Skinner's office - Skinner is there, even though it is at night. He just got out of the hospital. Doggett phones Mulder to tell him that Rorer is talking with Crane - Crane must be the one getting people past FBI security and feeding information to Billy. Crane, Rorer and Krycek must all be in league. Doggett calls Reyes from a phone inside the FBI, and Crane must have tapped the call. They know where Scully is, Mulder concludes.

Mulder says he has to get to Scully and protect her. Doggett relents and directs Mulder to Democrat Hot Springs in Northern Georgia. Mulder tells Doggett that Rorer and Crane may also be human replacements and that he and Skinner are in danger. Krycek interrupts the call by smashing the window of Mulder's car. He is holding a gun on Mulder and indicates that he plans to kill Mulder. Krycek says they have been on the same side all along and could have killed Mulder many times, but he hoped Mulder would win somehow. As Krycek begins the pull the trigger, Skinner, who has entered the parking garage unobserved, shoots Krycek. When Krycek continues to reach for the gun that has fallen out of his hand, Skinner shoots him twice more, the last time in the forehead. Krycek's last words are that it would take more bullets than Skinner can ever fire to win this game. Mulder still needs the exact location of Democrat Hot Springs from Doggett. Skinner sends Mulder off to find Scully, saying that he will "get it."

Upstairs, Doggett encounters Rorer and Crane, running to escape them. He runs downstairs, Crane chasing him. Doggett bursts out into the parking garage, encountering Skinner who turns and runs with him. They jump into Skinner's Blazer. Crane and Rorer run into the garage. Crane runs for the truck while Rorer runs for his own vehicle. Crane jumps on top of Skinner's car and beats in a window, grabbing at Doggett's throat. Skinner ends up driving past a roof support pillar, knocking Crane off the truck. Crane begins to get up, but Rorer drives through, his car bouncing right over Crane. The car bounces into another support pillar and explodes in flame.

Scully is in labor. The park ranger is helping more than Reyes, but Reyes notices a lump on the back of the ranger's neck. Reyes chooses her moment and smashes the ranger over the head with a pot in which they have been boiling water. Several other cars drive up and the ranger, now with facial burns, says, "This baby will be born." Reyes sees Billy getting up from the ground. Scully is in great distress. Billy and the others have all entered the room and are watching the labor. As she screams with pain, Scully is also screaming to not let them take her baby. The baby is born. Billy and the others leave. Outside, Mulder is approaching in a helicopter. He lands as the cars are driving off and Reyes summons him to the building where Scully is. Scully is OK, but she needs to get to a hospital, Reyes says.

Doggett and Reyes are in Kersh's office. He is expressing skepticism about their report. Who even assigned Reyes to the X-Files, anyway? Doggett answers that he assigned her because he is investigating Kersh's office for a late night meeting between Kersh, Rorer and Crane, both of whom are missing and presumed dead. Kersh is left without anything to say. Doggett and Reyes leave.

Mulder arrives at Scully's apartment. The Lone Gunmen are there, delivering presents. They don't understand how Mulder arrived in time to save Scully. Doggett told them that Doggett never reached Mulder with specific directions. Mulder says, "there was a light, I followed it." The Gunmen leave. Scully shows Mulder her son - he is perfectly normal. She has named him "William, after Mulder's father. Mulder holds him. Mulder jokes that the boy has Scully's coloring and her eyes, but that he looks suspiciously like Skinner - a reference to the bald head. Scully doesn't understand why they didn't take her son from her. Mulder isn't sure, but maybe little William isn't what they thought he was. That doesn't make him any less a miracle, though. From the moment Scully became pregnant, she was afraid about how and why it happened. Mulder says that there were many possibilities, but they both know the truth. "Which is what?" she asks. Wordlessly, Mulder kisses Scully on the mouth.

Note about dating: Evidence seen in this episode and the next indicates that The Lone Gunmen series finale cliffhanger All About Yves happens in the 48 hours between these two X-Files episodes. In Nothing Important Happened Today Langly's skin is dyed blue but in Existence it is not. In All About Yves we see the Romeo 61 list which includes recent entries on dates 5-14-01 and 5-4-01, indicating that this episode takes place not earlier than late May. The inconsistency of these dates versus Scully's 12 month pregnancy will probably never be addressed on screen.

Nothing Important Happened Today I.  A man, later identified as Carl Wormus, is having a drink in a bar. He dips his fingers into his glass and removes the ice. A striking dark-haired woman, later identified as Shannon McMahan, walks in and seats herself at the bar. Wormus moves over to talk with her. He wants his drinks without water, but the bartender always gives him drinks "on the rocks," he tells her. He doesn't like water because of an addative, "Chloramine," that the government adds to water. After only a few moments of banter McMahan suggests that they go outside "for some air." They are soon zooming down the highway in his convertible, apparently going to her home out in the country. Wormus slows as they approach a drawbridge because the bridge is rising. McMahan slams her hand down on his leg, flooring the accelerator. The car crashes through a barricade and falls into the water. Underwater, McMahan sits placidly in her seat as Carl struggles to release his seatbelt and swim to the surface. As he begins to rise out of his seat, McMahan grabs his ankle and holds him underwater.

It is 48 hours after last season's finale episode. Scully wakes early in the morning because little William is fussing. Someone is in the shower but we can't tell who. In the living room we see suitcases, all packed. The implication is that Mulder is also in the apartment and is preparing to leave. In rapid succession we see Doggett awake in his bedroom and Reyes awakened at her apartment by a phone call. The call is from Brad Follmer, an FBI assistant director who she once had a relationship with. He asks her to visit his office. Doggett makes coffee and hears a TV report of Wormus' death. He was a deputy administrator of the Environmental Protection Agency. Follmer is listening to the same report when he hears Reyes in his outer office. His assistant was away and she was going to leave a note rather than knock on his door. He attempts to kiss her and she resists, surprising him because a couple of years ago in New York she used to ask him to close the door so them could kiss. Doggett's investigation of assistant director Kersh is causing waves, Follmer tells her. He gives her two security tapes from the FBI building. One shows her meeting with Doggett. He doesn't immediately tell her the content of the other tape.

Doggett and Kersh meet each other on the elevator in the FBI building. Doggett says that his investigation is nothing personal. Kersh says that if Doggett can't find anything on him, nobody can. Doggett and Reyes talk in the X-Files office. He's upset that he is just doing his job but is getting a lot of heat. Reyes tells him that he may be unable to do his job – the second tape is from the FBI parking garage, where Doggett and Skinner were attacked, Rorer's car exploded and Skinner shot Krycek. The tape shows nothing but an empty garage. The garage has been cleaned of all evidence. Doggett goes to Mulder's apartment but it is vacant with all of Mulder's possessions removed.

At the Greater Maryland Water Reclamation Facility in Baltimore, McMahan emerges from a huge tank of water. She is nude. A plant worker, Roland McFarland, sees her fleetingly across the facility and walks to investigate. She grabs him and dives into the tank with him, pulling him deep underwater. Doggett arrives at Scully's apartment uninvited. The phone has been off the hook to keep from disturbing the baby and Doggett panicked that Scully may have disappeared also. Scully will not explain where Mulder went, just saying that he's gone. Reyes talks with Skinner.