Scully and Skinner begin to search for Mulder, but find themselves suspects in his disappearance. Agent John Doggett is heading the inquiry taskforce. Scully asks Skinner not to ruin his career by saying what he saw. Every time Scully sleeps, she dreams of an abducted Mulder being experimented on. Someone has been stealing computers and files -- Doggett thinks it is Mulder, but Scully suspects a cover-up. There seems to be a connection to the mind-reading boy [5.20 The End], and then Doggett discovers the boy with Mulder...
"Mulder" falls off a cliff, then disappears. Scully realises it's the bounty hunter, then Doggett sees two Scullys, and begins to suspect the truth. After lots of to-ing and fro-ing, Scully is attacked by the bounty hunter, but manages to kill him. He dissolves into a pile of green goo before any witnesses arrive. Doggett's report on the case earns him the displeasure of his boss, and he is assigned to the X Files as punishment.
Scully and Doggett investigate a bat-like killer who seems to have lain dormant for over 40 years. Scully is caught between her scientific scepticism, and feeling the need to play Mulder's role. Doggett starts sceptical, but even he has to believe when the creature attacks him.
Scully goes to investigate a murder, and ends up trapped in a backwater town tending a sick hitchhiker. The locals have infected him with a slug-like parasite they worship, but he is dying. So they infect Scully with it in his place. Doggett finds her just before the creature reaches her brain, and she realises she made a mistake not taking him in the first place.
A seven year old boy vanished ten years ago, and now reappears, but not a day older, and refusing to speak. Doggett tries to track down a kidnapper, but strange things keep happening, leading to a shallow grave in the woods.
A man accused of killing his wife finds that his days are running in reverse, and that he has been given the chance to correct his past mistakes. But he needs to convince Doggett and Scully -- every day.
Doggett investigates a cult leader who may be projecting himself into others' dreams. Scully goes to hospital.
A man is shot in a police cell through a wall. Scully thinks the killer may be able to see through walls. But Doggett investigates two strange brothers running a rat-extermination firm.
Scully and Doggett investigate a strange car crash that seems to have been caused by a dead man. Then they find he's still "alive", but turning to metal, and getting his revenge on the people who made him like this.
A legless Indian mystic who can manipulate minds travels to the US, and starts killing people, apparently in revenge for deaths due to a chemical leak back home. Two boys whose parents he killed try to stop him. Scully wants to believe, but can't trust her own eyes.
Doggett discovers Mulder was investigating a legendary man-eating creature just before he disappeared. He at first thinks that Mulder was trying to kill the creature to save a woman's life. But he then discovers the creature cures ills, that Mulder was trying to find a cure for his own brain disorder, but then realised curing made the creature suffer terribly, and tried to kill it himself to stop it suffering. Doggett takes the creature into protective custody, but the locals who are using it kill Doggett...
Scully and Doggett investigate a mysterious death in a Boston subway, under tight time pressure -- the trains will start rolling again soon. But the more they find out, the more it looks like a lethal infection. Doggett goes down underground with an expert crew, and Scully stays on top to advise -- and some of the crew dislike this arrangement.
A man comes to the FBI, claiming his abductee wife was killed by doctors when she had an alien baby. Her life history sounds identical to Scully's, and she starts to question her own pregnancy. Doggett investigates the man, and finds he is not all he claims to be, and may be a deep cover CIA mole. Another preganant woman appears, and Scully realises she is in danger, and takes her to a "safe" military hospital. But it seems it's all a set-up.
A group of cultists seem to be harming abductees, but in fact they are curing ones being returned. Then Mulder is one of the returned, but the FBI's investigations mean he doesn't get the cure. He's dead.
A former dead abductee, Billy, comes back to life, and so Skinner has Mulder exhumed, just to make sure. Despite being three month's dead and decaying, he is actually alive. The other abductee transforms into a new creature.Krychek appears, and offers Skinner a vaccine to cure Mulder, in exchange for terminating Scully's pregnancy. Skinner rips Mulder off life support instead, but that actually cures him.
Mulder is in perfect health, cured even of his brain problem, but is not allowed back on the X-Files, not that that stops him. He thinks Doggett is trying to cover up the truth. A census worker finds evidence of an alien invasion, replacing people with a certain DNA profile. Doggett gets the password to break into the census system from a contact, and passes it to Mulder via Scully. The Lone gunmen break Mulder in to the census centre, but it's a trap. Doggett goes in to get him out. Doggett's contact is, unknown to Doggett, an alien replacement.
Agent Reyes has a strange vision of ashes, and thinks it points to a connection between a recent double killing and the unsolved murder of Doggett's son. There is a suggestion of possession by some evil. Doggett does not want to believe. Scully suffers abdominal pains, and spends most of the episode hospitalised.
An oil worker dies mysteriously, and Mulder starts investigating on his own. When Doggett is sent to the oil rig, he finds Mulder there before him. Then Scully finds Black Oil in the dead worker's brain. Mulder and Doggett are trapped on the rig with infected workers. They destroy the radio that is calling the mother ship, then the workers destroy the rig. Mulder and Doggett only just escape, and the Deputy Director fires Mulder.
Doggett gets a new partner as Scully goes on maternity leave. She knows all about the X-Files, having processed Mulder and Scully's expense claims. But then they go missing while investigating a murder, after having found evidence that lizard venom was involved. Scully tells Mulder, who goes in search, and discovers the two agents, partially blinded by venom, trapped in the lair of a human/lizard, ready to become his next meal...
Billy, the abductee who came back to life just before Mulder, burns down a medical facility, and then kills Scully's first obstetrician. He's after Scully's baby, which appears to be not only fully human, but more so. Doggett, Mulder and Skinner try to protect Scully, with some help from Kryceck, who claims Billy and his kind (distinguishable by small spikes on the back of the neck, and the ability to survive being shot and run over) is a new kind of alien danger.