Scully attempts to decipher the strange symbols covering a submerged spacecraft, despite being swarmed by insects and seeing the sea turn to blood, in the hope of finding a cure for Mulder. He is still imprisoned by his own frenetic brain activity. Mulder has just enough control to ask Skinner for the help of a UFO whistle-blower. He realises Mulder has ESP, and needs a special drug to quieten his brain activity. Meanwhile, one of the scientists in Africa goes berserk, and Scully sees a vision of a strange old man. She returns to the US, and tells Mulder to hang on, she is near to an answer.
Mulder is still unconscious and dreaming, but then Cigarette-Smoking Man takes him away, to a safe house, where he experiences a normal life. But this too is just a dream -- he's actually the desired alien-human hybrid, and is undergoing surgery to extract his immunity to the alien virus, and have it transplanted into C-SM. Agent Fowler knows what's going on, and gives her security access card to Scully, who finds and rescues Mulder.
Scully and Mulder investigate a murder linked to a fast food restaurant, where the victim has had his brain eaten. They discover that one of the employees is a mutant, desperately trying to control an eating disorder -- he craves brains. Eventually he realises he cannot be what he is not, and jumps Mulder, so that he has to shoot him. [This is shot nearly entirely from the PoV of the mutant.]
As the year 2000 approaches, Skinner tasks Scully and Mulder with investigating four ex-FBI agents who have recently committed suicide, and who have been removed from their graves. Mulder suspects a connection with the apocalyptic Millennium cult, and seeks help from ex-member Frank Black. They discover the bodies have been reanimated as the Four Horsemen of the Apocalypse, ready to bring about end the world. Scully points out that the millennium isn't really until 1 January 2001, but "nobody likes a math geek". Scully is nearly throttled by a reanimated deputy. Mulder finds the four, kills one, but is trapped in a cellar with the remaining three. Frank Black arrives and kills two, Scully in the nick of time kills the last. The two agents -- finally! -- share a kiss, as they see in the New Year.
Frank Black: Lance Henriksen
A deputy sheriff is murdered with a single super-powerful blow to his head. The chief suspect, a sixteen year old boy, doesn't seem strong enough. And evidence goes mysteriously missing under the watch of a video camera. Then a teacher is killed by flying furniture in front of dozens of witnesses. Mulder and Scully discover a strange cave is giving a group of teenagers the power to move faster than the eye can see, along with an addictive high.
A builder of Rube Goldberg devices seems to be the luckiest man in the world -- he most improbably survives various murder attempts by mobsters whilst trying to win $100,000 for a friend's medical treatment. But he also seems to cause bad luck to those around him. Then he gets run down by a bus -- is this a sign his luck is running out?
Donnie Pfaster, a death fetishist who once nearly killed Scully , escapes from prison with the help of the Reverend Orison. The Reverend has his own plans for Pfaster, but then Pfaster escapes from his control, and hunts for Scully.
Orison: Scott Wilson --- Don Pfaster: Nick Chinlund
A magician spins his head through 360 degrees, and a few minutes later is found dead, with his head neatly severed. Mulder and Scully investigate, and find the magician's wheelchair-bound twin brother, a rival magician, a poker debt, and a bank robber, may all be involved in the last great magic act.
Maleeni: Ricky Jay
Snakes are killing the unrighteous, but is it really a case of divine intervention? Or is the snake-handling leader of a charismatic church somehow involved?
A little girl, Amber Lynn, is kidnapped under strange circumstances: no break in to the house, a locked bedroom, and a kidnap note written automatically by the mother, saying "No-one shoots Santa Claus". Mulder remembers a similar case a decade earlier. Then his mother commits suicide after leaving him a cryptic phone message. Mulder is convinced she was murdered to keep her quiet about his sister, but Scully does the post-mortem, and discovers she had a horrific terminal illness. Mulder's confidence is shattered. Then the kidnapped girl returns to her mother in a vision, sending a clue that leads the agents to Santa's Grotto, where a man has videos of the missing children.
The agents arrest the man who has abducted and killed many children, but he claims he didn't kill Amber Lynn. A police psychic offers help. He has a theory that some children about to die are rescued and taken elsewhere by star spirits. Scully discovers the original search for Samantha was stopped by order of Cigarette Smoking Man. He tells her it was because he knew Samantha was dead. At an abandoned airbase, Mulder discovers Samantha's diary. Cigarette Smoking Man's team had been doing tests on her after her abduction, but she escaped them when she was about 14. Then she was taken by these spirits just before the team could recapture her. Mulder discovers these children are dead, in a kind of paradise, and is reunited with the spirit of his sister. The psychic refuses to believe, because he is trying to find his own son.
A "Cops" fly-on-the-wall documentary team stumble across Mulder and Scully investigating what may be a werewolf. The FBI "has nothing to hide" (despite Scully's constant attempts to stop Mulder spouting off about the paranormal on camera), so the film crew is permitted to follow them, and we see the whole investigation through the crew's eyes, or lens.
A gamer is impossibly killed during a VR game. The Lone Gunmen, stakeholders in the company, call in Mulder and Scully to help. A strange female character is suspect, then another world-famous gamer dies. Mulder, keen to play, goes into the game to investigate, and becomes trapped. Scully, less enthusiastic about VR games, follows him in to save his life.
A popular doctor's family is being struck down one-by-one by obscure illnesses. Mulder discovers hexcraft is involved, performed by a mountain man who blames the doctor for his daughter's death. Scully takes the doctor and his daughter to a hideaway -- but then the man uses his craft to blind her while he attempts to kill the doctor.
Cigarette Smoking Man offers to show Scully the cure for cancer, but only if she hides her trip from Mulder. She goes with him unwillingly, trying to send Mulder clues. But it is a con to trick the owner of the cure into giving up his secrets. Strangely, CSM stops his accomplice from killing Scully, but still steals the data disc from her, yet throws it away in the end.
Over Easter, Mulder investigates a mysterious death involving croaking ravens, shattered mirrors, and a murderous creature. Scully is left on an uncomfortable stakeout, searching for what Mulder thinks may be a female serial killer who can disappear, but who turns out to be a male preacher in drag.
Mulder is away in England investigating crop circles (including a reference to the Cambridge Mandelbrot !). A series of "accidents" make Scully re-examine some choices she has made, and to try alternative medicine to save the life of her former teacher and lover. [Written and directed by Gillian Anderson.]
A man about to testify against a power cigarette company is found dead with his face eaten away. A second person dies, covered in mutant tobacco beetles. Then Mulder falls victim, with beetle larvae growing in his lungs. Skinner discovers a "safer cigarette" research programme has gone disastrously wrong. Scully must work out the cause and the cure before Mulder dies.
A Hollywood screenwriter, and old college friend of Skinner, shadows the agents as they investigate a church bombing, and turns it into a film, in which "Mulder" and "Scully" fight zombies, defeat the Cigarette Smoking Pontiff, and then make out in a coffin. The real story was only a little more prosaic.
"Agent Mulder": Garry Shandling -- "Agent Scully": Tia Leoni. Written and directed by David Duchovny
Two identical women, doppelgangers, leave a trail of violence and destruction wherever they travel. Now they are in Kansas, both in love with the same man, both unwilling to move on. Then Scully tracks down their sperm-donor father...
A man with no mouth makes Mulder think he is on the track of a genie, and the invisible corpse convinces him. An excited Scully invites some scientists to come and look at the corpse, but of course when they arrive it has disappeared. Mulder tracks down the genie, who grants the conventional very literal three wishes. His first wish goes devastatingly wrong, but he thinks he can out-Fox her.
"In the seven years we've been working together I've seen some amazing things, but this takes the cake."
Amidst rumours of a downed UFO, the agents investigate the present day disappearances of the Oregon abductees that they first encountered seven years ago . A dying Cigarette Smoking Man sends Krycek to find the ship, in order to rebuild the conspiracy. As more past abductees vanish, and Scully keeps fainting, Mulder is worried she might be next, and sends her away. But it is Mulder, with his abnormal brain activity , who is in danger. He is abducted by the alien bounty hunter and flown off in a UFO right under the startled gaze of Skinner. After Scully faints again whilst consulting the Lone Gunmen, she discovers she is pregnant.
Scully: "I have seen things I can't deny." -- but it took 7 years-worth of evidence!