In Washington, D.C., Agent Fox Mulder appears before an FBI panel regarding his experiences in Antarctica. Assistant Director Walter Skinner (Mitch Pileggi) tells Mulder that he and Scully have been denied reassignment to the division. Mulder goes to his former basement office, only to discover that Jeffrey Spender and Diana Fowley (Mimi Rogers) have been assigned to the X-Files. Going against orders, Mulder and Scully track down an escaped alien in Phoenix, Arizona while Cigarette Smoking Man (William B. Davis) gives chase. Mulder and Scully eventually discover that Cigarette Smoking Man has been using Gibson Praise to locate the creature. Scully brings Gibson to the hospital, where it is determined that he has the alien virus in his blood. Later, Skinner is mysteriously poisoned by a nanorobot infection. The culprit is revealed to be Alex Krycek (Nicholas Lea), a rogue FBI agent who formerly worked for the Syndicate, who continues to control the potentially debilitating nanotechnology in Skinner's system in order to achieve his goals.
Mulder and Scully later learn of reports of rebel aliens burning doctors who were working on Cassandra Spender (Veronica Cartwright), an alien abductee and mother of Jeffrey Spender. Skinner takes Spender to the scene, where Cassandra asks for Mulder. She informs Mulder and Scully that the aliens are here to destroy all life on Earth. She claims that a rebel force of aliens is mutilating their faces to prevent infection by the black oil. Cigarette Smoking Man reveals everything to Diana Fowley, who agrees to help him and betray Mulder. Cassandra later escapes from a hospital and arrives at Mulder's apartment, demanding that he shoot her because she is the embodiment of fifty years of work by the Syndicate—an alien-human hybrid that will trigger colonization if the aliens learn of her existence.
Fowley arrives and forcibly takes Mulder, Cassandra, and Scully to a CDC facility at Fort Marlene. There, Mulder runs into Marita Covarrubias (Laurie Holden). Marita tells Mulder that she was subjected to Syndicate-run black oil vaccine tests. Meanwhile, the Syndicate rendezvous at a checkpoint, preparing to be taken away by the Colonists, who are prepping for invasion. However, they are met by the alien rebels, who incinerate them all, including Cassandra; Cigarette Smoking Man and Fowley escape. Jeffrey Spender is then purportedly killed by Cigarette Smoking Man.
Several months later, a metallic artifact with inscriptions is discovered on the beach of Côte d'Ivoire in Africa. After Mulder examines rubbings of the object, he begins suffering from a headache, seemingly caused by the rubbings. Mulder's condition worsens, but he gains telepathic abilities. Chuck Burks (Bill Dow) tells them that the symbols on the artifact are Navajo. Eventually, Mulder passes into an aggravated delusional state and is placed under observation at a hospital. Hoping to find an answer, Scully rushes to Africa and finds the massive wreck of a large spacecraft partially buried in the beach.
|No.||Episode Name / Summary|
Just after having returned from Antartica, Mulder and Scully conduct an unofficial search for a vicious alien in Phoenix, Arizona.
Mulder finds himself forced to drive a man in a high-speed dash across the Southwest in an effort to prevent the man's head from exploding.
Lost in the Bermuda Triangle, Mulder believes he has traveled back to 1939 and has to evade Nazis aboard an historic British sailing ship similarly lost, encountering individuals who seem strikingly familiar to him.
On a tip, Mulder and Scully visit the infamous Area 51 where a strange event swaps Mulder's personality with that of Morris Fletcher, a shadowy government agent.
Scully desperately tries to reverse the personality switch between Mulder and Morris Fletcher before it's too late.
|6X06||"How the Ghosts Stole Christmas"
On Christmas Eve, Mulder and Scully go ghost-hunting in a supposedly haunted house full of Christmas spirit.
|6X07||"Terms of Endearment"
Mulder believes that a bigamist, suspected of pre-natal infanticide, is actually a demon.
|6X08||"The Rain King"
A man in Kansas claims to be able to command the weather and appears to be the real deal.
Skinner is infected with a strange disease triggered by nanotechnology in his body.
Scully is partnered with another agent and assigned to investigate a crime scene photographer but her encounter with him leads to deathly consequences for them both.
The unexpected return of Cassandra Spender and an attack by alien rebels forces the Syndicate's hand in a move that threatens the survival of their carefully-crafted conspiracy.
An alien rebellion leads the Syndicate to its demise as their twenty-five year conspiracy approaches its disastrous collapse.
Agent Dales contacts Mulder to find out happened in the Shipley residence, from where Dales received a description of a creature with tentacles that took her husband. Mulder and Scully while returning gets stuck in an apartment in the midst of Hurricane Leroy. They soon discover that the same creature might be in the plumbing.
A woman is trapped in an endlessly repeating time loop that ends in a tragic bombing in which Mulder and Scully lose their lives every time.
Mulder and Scully go undercover as a married couple in a gated community to investigate the mysterious disappearances of neighbors who didn't conform.
Mulder and Scully investigate a series of attacks by a canine that shows signs of human intelligence.
The agents pursue an escaped convict who is capable of passing through solid matter and is desperate to meet his son for the first time.
A writer who lives next door to Mulder becomes the prime suspect in a series of killings.
Arthur Dales, the brother of a retired FBI agent with the same name, tells Mulder about an alien who played baseball for the Roswell Grays in 1947.
|6X20||"Three of a Kind"
The Lone Gunmen encounter Susanne Modeski while infiltrating a defense contractors' conference in Las Vegas.
A mystery involving two skeletons leads the agents on a journey in which nothing is quite as it seems.
Mulder believes that metallic objects discovered in Africa are proof that life originated elsewhere in the universe.
- David Duchovny as Special Agent Fox Mulder (22/22 episodes)
- Gillian Anderson as Special Agent Dana Scully (22/22 episodes)
- Mitch Pileggi as Assistant Director Walter Skinner (8/22 episodes)
- Chris Owens as Special Agent Jeffrey Spender (5/22 episodes)
- William B. Davis as Cigarette Smoking Man (5/22 episodes)
- Nicholas Lea as Alex Krycek (4/22 episodes)
- James Pickens, Jr. as Deputy Director Alvin Kersh (6/22 episodes)
- Tom Braidwood as Melvin Frohike (5/22 episodes)
- Dean Haglund as Richard Langly (5/22 episodes)
- Bruce Harwood as John Fitzgerald Byers (4/22 episodes)
- Mimi Rogers as Special Agent Diana Fowley (4/22 episodes)
- Michael McKean as Man in Black Agent Morris Fletcher (3/22 episodes)
- Don S. Williams as First Elder (3/22 episodes)
- Wayne Alexander as G. Arnold (2/22 episodes)
- Veronica Cartwright as Cassandra Spender (2/22 episodes)
- George Murdock as Second Elder (2/22 episodes)
- This was the first season that was filmed in Los Angeles.