While Scully travels to Africa to piece together the meaning of the symbols on the spaceship beached on the Ivory Coast, Mulder is imprisoned by his own frenetic brain activity. He manages to get a message to Skinner who finds Kritschgau and together they try to understand what is happening to Mulder before it is too late.
Scully frantically searches for a way to help her ailing partner without having anyone to turn to for help, while a catatonic Mulder’s dreams lead him away from his mission and the X-Files to a place which he believes is a better life.
A fast-food restaurant is linked to the discovery of a submerged car with a body in the trunk, but no brain in the body. Mulder and Scully investigate further and find that a monster is trying to live a normal life but sometimes has to kill people because of the hunger.
As the year 2000 draws closer, the agents are up against a man from the Millennium Group who believes that he can bring about the end of the world on the 31st of December if he resurrects 4 former members from the dead. To gain more insight into the group and its practices, Mulder and Scully enlist criminal profiler Frank Black to assist them in the investigation.
A teenage killer eludes Mulder and Scully by moving too fast for the human eye. Slowly Mulder and Scully realise his ability and try to work out how he gained his power, but not before he goes after his own father, who happens to be the town sheriff. It appears that the killer likes to prey on the emotional vulnerabilities of impressionable kids but can Mulder and Scully put a stop to it before it’s too late?
Mulder and Scully are caught in a real-life Rube Goldberg device as they investigate a man cursed with extremely good luck since he survived a plane crash back in 1989. The man, Henry Weems, insists that he is never unlucky but he finds out that he cannot pass on his good luck to others without severe consequences to their part.
A series of prison breaks bring Agents Mulder and Scully face to face with Scully’s former kidnapper, Donnie Pfaster, as Scully is forced to question her faith and confront the clash of morality and religion. But Scully soon learns that Donnie is very keen on going after the one victim that managed to escape him, Dana Scully when Reverend Orison breaks him out of prison…
When a small-time magician performs a trick where it appears that he turns his head all the way around but is then found in his van dead with his head neatly sawn off, Mulder and Scully suspect he was murdered and get caught up in an intricate scheme planned by two magicians trying to rob a bank.
Mulder and Scully investigate a gruesome and unexplained snake-bite death, which points to a religious group in the Deep South. Before long the agents realise that the snakes are being used to kill the unrighteous.
A young girl unexplainably disappears from her home and Mulder requests the case even though it is a full FBI matter, not just an X-File. When Mulder takes some outrageous leaps to convince the girl’s parents that she will be found, Scully fears that Mulder is becoming too personally involved with the case because of his sister’s abduction.
After arresting the murderer of Amber-Lynn LaPierre and discovering a mass gravesite containing the bodies of dozens of missing children, a man comes to Mulder and claims to have had visions of other victims who aren’t buried at the site. Despite Scully’s objections, he takes Mulder on a journey which reveals what truly happened to his sister.
A Los Angeles police officer who is being filmed for the show COPS is attacked by a strange monster and Mulder and Scully are investigating the case. Scully is wary of having their faces put on national television but Mulder welcomes the publicity.
The Lone Gunmen call Mulder and Scully to a Virtual Reality development lab where they learn that one of the program testers was killed inside the computer generated game environment by the digital image of a woman. Needing to get his yah-yah’s, Mulder enters the game to fight the woman but Scully must step in to save him.
Mulder and Scully are called in to investigate a series of murders where the victims are all in some way related to a wealthy, well-educated doctor. As they search for clues the FBI agents discover the apparent motive is revenge. Years ago the doctor was involved in the euthanasia of a young girl on the verge of death. Once again, Mulder must race against time to find who is behind the killings before the doctor and (more importantly) Scully become the next victims.
After the miraculous recovery of a young boy who had cancer, Mulder and Scully investigate what has happened but Scully is shocked when The Smoking Man tells her that he cured the boy and offers to show Scully the cure for cancer if she travels with him. But hides her trip from Mulder.
As Mulder investigates a missing person case with a key feature being a menacing raven, he learns to enjoy the creature comforts of a well-tended home while Scully must tough it out on an uncomfortable stakeout.
A series of coincidences puts Scully in contact with someone from her past, a married man who she once had an affair with during medical school, but is dying. This causes her to question her romantic and professional choices in her life. Meanwhile Mulder investigates crop circles.
When an employee of Morley Tobacco Co. is apparently killed by tobacco beetles, Mulder suspects that the beetles have hatched inside his lungs and found their way there through inhalation of smoke from an experimental cigarette.
Mulder and Scully watch a movie with themselves as characters and are thoroughly disgusted at how they and their case are portrayed on the big screen. They recount how 18 months earlier they were followed around by a Hollywood producer while investigating a case concerning ‘The Lazarus Bowl’ a mythical piece of pottery reputed to have inscribed on it the words that Jesus Christ spoke when he raised Lazarus from the dead.
The Agents cross paths with a pair of doppelgangers whose close proximity with each other leaves a trail of destruction across 17 states. Mulder and Scully must first understand why this is happening before they can stop it. But the Agents soon realise that the only way to stop the destruction is by stopping the girls meeting up, but this becomes difficult when both fall in love with the same man.
Mulder and Scully discover a jinniah (genie) in a rug who, after 500 years of granting wishes, has come to the conclusion that people are still as greedy and self-centered as they always have been and she begins to corrupt the wishes she grants if they are not ‘specific’ enough.
Mulder and Scully return to the town of their first X-Files investigation where a UFO has crashed in the forest. CSM arranges for Krycek to be released from prison in order for him to make contact with the aliens and begin rebuilding the ‘Project’, while Scully’s health appears to be taking a turn.