When a small town church is the site of a number of ritualistic-like murders, fingers are pointed to the Church of God with Signs and Wonders, a church where the Bible is read literally, and punishment is dealt deftly. But soon the agents realize that the difference between the peaceful religious and the fanatics may not be very much at all.
"Sein und Zeit"
While investigating the bizarre disappearance of a young girl from her home, Mulder becomes obsessed with a number of children who have vanished in similar ways. Scully's fears that he is emotionally involved due to his sister's disappearance 27 years earlier are heightened when Mulder's mother dies, apparently of suicide.
As Mulder is forced to accept that his mother’s death was by her own hand, he is led by a man whose son disappeared years earlier to another truth—that his sister may be among the souls taken by ‘walk-ins’, saving the souls of children doomed to live unhappy lives. Together, they embark on a journey that will reveal to Mulder the truth about his sister’s disappearance.
A filming of an episode of COPS gets in the way of the collaborative effort between the FBI and the local police department. Mulder later finds out that the monster feeds on fear. While Mulder embraces the publicity, Scully is not so sure of it. The episode was filmed as if it was an authentic episode of the TV series COPS.
When a school student becomes the prime suspect in the bizarre murder of a police officer, Mulder and Scully are sent to investigate. They discover that the boy and a couple of friends have been playing with the ability to accelerate their movements to a frequency the human eye can’t perceive.
"The Goldberg Variation"
After being thrown off a building and surviving, Henry Weems, who appears to be the luckiest man in the world, attracts the attention of Mulder and Scully. But, if he is so lucky, why is he on the run from the mob, and why is everyone around him so unlucky?
Reverend Orison releases Donnie Pfaster, Scully’s former kidnapper, as seen in the second season episode "Irresistible", from jail in the hopes of passing judgment on him. What he discovers instead is that he has released pure evil, and it’s headed for Scully.
"The Amazing Maleeni"
The Amazing Maleeni, a small-time magician, performs an amazing feat to impress a heckler—he turns his head 360 degrees. So when he is later found without a head at all, Mulder and Scully arrive on the case and discover an angry ex-con, an unimpressed rival, and Maleeni’s twin brother all seem to have something to do with the plan to rob a major bank.
Walter Skinner (Mitch Pileggi) and Michael Kritschgau (John Finn) work desperately to attempt to discover what is wrong with Fox Mulder (David Duchovny), who is imprisoned by his own frenetic brain activity, but they are unaware of Agent Diana Fowley’s (Mimi Rogers) duplicity. In the meanwhile, Dana Scully (Gillian Anderson) is hunting for an ancient artifact in Africa.
"The Sixth Extinction II: Amor Fati"
Returning to Washington to find Mulder gone, Scully joins Kritschgau and Skinner—who is still being forced into betrayal by Alex Krycek (Nicholas Lea)—to find her partner. However, the Cigarette Smoking Man (William B. Davis) has taken Mulder to a place where all his problems are gone and Fowley is forced to make a choice about her loyalties.
In an episode told from the point-of-view of the “monster”, a fast-food employee with unusual cravings becomes the focus of an FBI investigation. The victims appear with no brain and a suction hole in the forehead.
An associate of the Millennium Group, which believes the apocalypse will happen on the new year of 2000, resurrects the dead for use in the bringing about of the apocalypse, and Mulder and Scully have to ask the help of criminal profiler Frank Black (Lance Henriksen), a man who has former experience with the shadowy group.
The skeletonized remains of a young couple are found in the fields of North Carolina. When Mulder and Scully go to investigate, they find that a giant fungal life form releases an LSD-like drug into the air with spores, and then slowly digests its victims. Mulder and Scully fall into its trap and are not sure of what is reality and what is fantasy.
Mulder believes that metallic objects discovered in Africa are proof that life originated elsewhere in the universe. Skinner, now in contact with Alex Krycek and Agent Fowley, begins monitoring Mulder and Scully on the case. Mulder, due to the apparent influence of the artifact, falls mentally ill, which leads to Scully travelling to Africa alone.
After a prison camp is destroyed by a tornado, an escaped inmate is suspected of killing the warden. As the inmate hunts down his old girlfriend, he finds out where his child is and attempts to take him back. Mulder and Scully set out to find him and discover that he has the ability to pass through conductive materials.
A series of murders takes place where the heart has been removed from the victims. A writer that lives next door to Mulder is writing a novel about the murders before they actually happen. Scully finds herself confused and drawn to the writer, who has a romantic interest in her.
While working in Roswell, New Mexico in 1947, young cop Arthur Dales (the brother of the Arthur Dales who started the X-Files) stumbles across a "negro" baseball player who is actually an alien with a love of the game hiding among humans.
"Three of a Kind"
While at a conference in Las Vegas, The Lone Gunmen run into the enigmatic Susanne Modeski. After deceiving Scully into joining them, the trio soon find out that Susanne’s fiancé is planning to use her new brainwashing drug for political assassinations.