The X-Files are no more. Shut down by the FBI, Scully and Mulder have been reassigned. New supernatural events prove that the X-Files investigations are a necessity and Walter Skinner restores them but with a new team, Fox Mulder and Alex Krycek. Mental patient and alien abductee Duane Barry kidnaps Scully and takes her to a mountain where she disappears. Krycek murders Barry. He works for the Cigarette Smoking Man and disappears with his true loyalties revealed. Scully is returned on the edge of death and Mulder faces a critical choice, seek to ambush members of the conspiracy with the help of his new source Mr. X or stay by Scully's bedside. He chooses Scully. Scully recovers and rejoins Mulder on the X-Files.
Men of identical appearances are being murdered by an alien bounty hunter. They learn that they are not exactly Human but some sort of alien-human hybrids made in a lab. That they are identical because they are clones. Mulder and Scully's attempts to protect them are futile because the alien bounty hunter can change form to get at them. Mulder isn't focused on any of this though because the Cigarette Smoking Man shocks Mulder by introducing him to his long missing sister, Samantha Mulder. Scully is captured by the shape shifter. An exchange is set up with the help of AD Walter Skinner. Samantha will trade herself to the alien bounty hunter for Scully. Skinner deploys sharpshooters to take down the alien bounty hunter but when he is shot he takes Samantha with him. When they retrieve her body, it dissolves into a green liquid. Mulder realizes she was a clone, like the men who were murdered by the bounty hunter. He finds other Samantha clones who reveal that some alien-human hybrid clones were made to establish a colony on Earth but the alien race finds these part Human hybrids to be abominations to the purity of their kind so they sent the alien bounty hunter to exterminate them. The bounty hunter arrives, knocks out Mulder, kills the other Samantha clones and burns their laboratory. Mulder doggedly pursues the alien bounty hunter back to his ship, desperate for information on his sister, but fails to defeat the mighty alien bounty hunter. He succeeds in breathing in the toxic fumes of the bounty hunter's blood and hears this from the bounty hunter, "She's alive. Can you die now?" Scully manages to rescue Mulder from the Beaufort Sea and save him from the effects of the toxic blood.
At a Navajo reservation in New Mexico an earthquake reveals a boxcar buried in the ground. Inside are strange corpses. A hacker called the Thinker secretly meets with Mulder to give him the top secret files of the government's knowledge of aliens. This starts a firestorm among the Syndicate members. The Cigarette Smoking Man lies and says it is already handled. Mulder is asked if he has the digital tape this hacker had and he attacks Skinner. He could be dismissed from the FBI over this. Elsewhere, William Mulder meets with the Cigarette Smoking Man who suggests Mulder may have the tape. Scully begins trying to translate the tape since it is in a Navajo code like those used during World War II. Mulder's father asks Mulder to visit him but before he can reveal the secrets he is ashamed of, he is murdered by Krycek. He dies in Mulder's arms, begging for forgiveness. He calls Scully who tells him to flee. She suspects he is being set up which is why she tests his gun but Mulder assumes Scully is working against him. Krycek is about to be killed by Mulder at his apartment when Scully shoots Mulder.
Mulder awakens in New Mexico and Scully informs him that he was acting so aggressively because they were drugging his water supply. The water supply of the whole apartment building. She introduces Mulder to Albert Hosteen, an old code talker who has started translating the files. They refer to some sort of test. Albert's grandson Eric Hosteen drives Mulder to the boxcar. He goes inside and finds a pile of bodies of creatures that don't look Human but they have smallpox vaccination scars. The Cigarette Smoking Man arrives with soldiers and search the boxcar. They don't find Mulder so they burn the boxcar. Where could he have gone? He was in there!
To Be Continued in Season 3.
|No.||Episode Name / Summary|
|2x01||"Little Green Men"
With the X-files closed, Mulder is contacted by a political ally and sent on a dangerous mission to a radio telescope in Arecibo, Puerto Rico.
While continuing work not related to the X-files, Mulder apparently finds evidence of a giant worm-like monster in the New Jersey sewage system.
Apparently prompted by messages from digital appliances with instructions to kill, several residents of a small farming community suddenly turn violent and dangerous.
A new partner joins Mulder as he investigates the deaths of several victims who were killed by apparently nonexistent forces.
|2x05|| "Duane Barry"
Mulder becomes involved in a hostage situation with an escaped psychiatric patient who claims to be terrified of frequent alien abductions. (Part 1 of 2)
Mulder attempts to search for Scully when she is abducted by Duane Barry, the escaped mental patient who recently held Mulder hostage. (Part 2 of 2)
With Scully missing, Mulder closes in on an "Unholy Trinity" of vampiresque killers and finds himself falling for a mysterious woman who is the prime suspect.
Scully miraculously appears in a Washington DC hospital, unknowingly supervised by a nurse who may never have existed.
When a moving shadow appears on a video transmission from a volcano, a volcanologist asks Mulder and Scully to investigate the incident.
The agents investigate a suggested link between a religious cult of vegetarians and the abduction of several teenagers, although they find that the disappearances are actually connected to a deadly event in their own past.
Mulder and Scully uncover strange occurrences in an old-age care home when one of the nurses is attacked by an unseen force she claims to be one of the residents, a 74 year old man.
When a detective mysteriously uncovers the remains of an FBI agent who disappeared in the 1940s while investigating a murder case similar to a modern-day one she is investigating, Mulder and Scully believe that the original killer had passed his genetic trait of violence to his grandchild.
A mortuary worker who collects hair and fingernails from dead bodies begins to kill people to expand his collection, and he sets his sights on Scully.
|2x14||"Die Hand Die Verletzt"
After a teenager is ritualistically murdered in a small town, Mulder and Scully are caught up in a secret occult practice within the local PTA and a substitute teacher with odd powers.
After several murders occur within a Haitian refugee camp, Mulder and Scully are caught in the middle of a secret battle involving a Voodoo priest and the camp commander.
After four identical men are killed and their obituaries are e-mailed to Mulder, a mysterious CIA agent informs him and Scully that the killer is a bounty hunter sent to destroy the start of a colony of clones. Meanwhile, Mulder is distracted when his sister, Samantha, suddenly returns. (Part 1 of 2)
Mulder and his sister race to evade the alien bounty hunter and uncover more of the insidious conspiracy. (Part 2 of 2)
Strange things happen in a zoo that result in several deaths, including a government employee and apparently an invisible elephant.
In the North Atlantic, Mulder and Scully investigate the crew of a US Navy Ship, all of whom somehow radically aged. The agents locate the ship but, like the vessel's crew before them, Mulder and Scully also suffer from rapid aging.
A bizarre murder in Florida brings Mulder and Scully to a town populated by circus freaks and sideshows performers of all shapes and sizes, bringing into question the very definition of "normal."
With Scully's help, Mulder investigates a strange death that he believes may be an example of poltergeist activity.
After several men in a prison die of a mysterious illness, Scully tries to discover the cause while Mulder attempts to find two escapees who could potentially spread the disease.
Mulder and Scully encounter a man who is afraid of his own shadow.
Mulder and Scully investigate the disappearance of man in a town where the residents really are what they eat.
A computer hacker discovers evidence against the Syndicate that is so damning that its revelation to the public would be nothing short of catastrophic, leading Mulder into a race against sinister agents to learn the truth. (Part 1 of 3)
- David Duchovny as Special Agent Fox Mulder (25/25 episodes)
- Gillian Anderson as Special Agent Dana Scully (24/25 episodes)
- Mitch Pileggi as Assistant Director Walter Skinner (9/25 episodes)
- Steven Williams as X (7/25 episodes)
- William B. Davis as Cigarette Smoking Man (6/25 episodes)
- Nicholas Lea as Alex Krycek (4/25 episodes)
- Tom Braidwood as Melvin Frohike (4/25 episodes)
- Bruce Harwood as John Fitzgerald Byers (4/25 episodes)
- Dean Haglund as Richard Langly (3/25 episodes)
- Peter Donat as William Mulder (3/25 episodes)
- Sheila Larken as Margaret Scully (2/25 episodes)
- Megan Leitch as Samantha Mulder (2/25 episodes)
- Steve Railsback as Duane Barry (2/25 episodes)
- Brian Thompson as Bounty Hunter (2/25 episodes)
- Michael David Simms as Senior FBI Agent (2/25 episodes)
- Andrew Johnston as Special Agent Barrett Weiss (2/25 episodes)
- Christine Willes as Karen Kosseff (2/25 episodes)