As Mulder lies in a neurological unit, his brain under attack by a deadly onslaught of electrical impulses, Scully struggles to decipher strange symbols covering a spacecraft found submerged off West Africa's Ivory Coast. But the connection between these two phenomena is just the first of many challenges the agents are destined to confront. For they are about to enter a time of closure and a time of new beginnings. For Mulder there's the death of his mother and Diana Fowley, and the end of his search for his abducted sister, Samantha. For Scully it is a time to face her own personal demons, among them the return of death fetishist Donnie Pfaster. Yet just as Scully faces the ultimate new beginning, the ultimate horror occurs — the abduction of Mulder.
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 monster who feeds on human brain matter tries to lead a normal life, but he soon cannot control his feelings of 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 four 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 young man who has gained the ability to move faster than the eye can see begins to use his new power to kill his enemies, including the local sheriff who happens to be his father.
Mulder and Scully get caught in a real-life Rube Goldberg device when they meet Henry Weems, who just may be the luckiest man on Earth - except everyone around him doesn't seem to be that lucky.
Reverend Orison hopes to save Donnie Pfaster's soul by helping him break out of prison, but Donnie immediately plans to go after the victim that once escaped him... Scully.
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 sawed 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.
Snakes are killing the unrighteous, but Mulder and Scully doubt that this is a case of divine intervention.
A young girl inexplicably 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 grave site 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 suspect that hexcraft is the source of threats against a doctor's family.
The Cigarette-Smoking Man offers to show Scully the cure for all diseases if she travels with him, but on one condition: Mulder must not know about her trip.
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 leads Scully to a married man she had an affair with during medical school but left him to protect his family.
While protecting a man due to testify against the Morley cigarette company, Skinner is horrified when the witness dies mysteriously. What the agents soon discover is that a new brand of cigarette has a dangerous secret.
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.
Mulder and Scully cross paths with two women who are identical and have followed each other across 17 states in the last three years, causing chaos and mayhem wherever they are.
Mulder and Scully discover a 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. The Cigarette-Smoking Man 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.