The exploits of FBI Special Agents Fox Mulder and Dana Scully who investigate X-Files: marginalized, unsolved cases involving paranormal phenomena. Mulder believes in the existence of aliens and the paranormal while Scully, a skeptic, is assigned to make scientific analyses of Mulder's discoveries that debunk Mulder's work and thus return him to mainstream cases.
Mulder and Scully head to Ellens Air Force Base to investigate the mysterious case of a military test pilot who disappeared after experiencing strange psychotic behavior. While on the case, Mulder meets a mysterious man dubbed 'Deep Throat' who claims to have classified information about his investigations into the paranormal.
As Section Chief Blevins expresses his concern with the direction of the X-Files, Mulder becomes obsessed with solving a case that closely parallels an encounter he experienced as a child: the abduction of his kid sister, Samantha.
Mulder puts the future of the X-Files in jeopardy when he heads to a UFO crash site being rapidly covered up by the military. He is arrested, and while in jail he meets Max Fenig, a UFO nut whose NICAP group has followed Mulder's work on the X-Files. When Mulder is released, Scully urges him to return to Washington to face his superiors and try to save his job, but Mulder finds out that Max is more than meets the eye and ignores Scully to try and save him instead.
When two fathers on opposite sides of the country are inexplicably murdered at the exact same time in the exact same way, Mulder and Scully are called in to investigate. When they discover that the two fathers' eight-year-old daughters are identical twins, they realize that something even stranger is going on.
An old Oxford girlfriend of Mulder's asks for his help on an international case concerning the unexplainable execution of several British dignitaries, and they encounter an assassin who can produce fire from his bare hands.
When death row inmate Luther Lee Boggs claims to be psychic and can lead Mulder to a serial killer in return for a lesser sentence of life in prison, Scully becomes an unwilling believer when Boggs tells her that she can communicate through him with her recently deceased father.
A series of sexually-oriented murders, which are identical except that the killer appears to be both male and female, draws Scully and Mulder to an Amish-type community of people called the Kindred.
When FBI Agent Jack Willis and bank robber Warren Dupre are both shot at the same time during a robbery attempt, Dupre dies when Willis is brought back to life. When Willis rushes out of the hospital and begins acting strangely, Mulder concludes that Dupre has come back to life in Willis' body.
Mulder becomes the target of someone from his past named John Barnett. He was a jewelry store robber with an itchy trigger finger that Mulder sent to prison when he first joined the Bureau. The only problem is that Barnett died four years ago.
Mulder and Scully receive information from Deep Throat about a UFO that was shot down over Iraq and has been secretly transported to the US. However, Deep Throat then intentionally misleads the agents to prevent them from discovering the truth.
Mulder and Scully travel to a Native American reservation to investigate the death of a man who was mistaken for a wild animal and may have been the legendary Manitou, a man who can shape-shift into a beast.
When a group of loggers in the Washington State National Forest disappear in the same way that another group disappeared 50 years ago, Mulder and Scully go along to investigate and find themselves trapped in a cabin surrounded by flesh eating insects that only attack at night.
Eugene Tooms is released from the sanitarium, and Mulder becomes personally involved to ensure that he is caught in the act of getting the last human liver he needs to go into hibernation for another 30 years.
After a detective and his former partner die in unexplained circumstances, the accidents are linked to a little girl who witnessed both deaths. Mulder believes that she may be the reincarnation of a policeman murdered by his colleagues.
Mulder and Scully investigate the death of a scientist working on advanced propulsion technology. The mentally challenged janitor Roland, who has secretly been completing the scientist's work, is the prime suspect.
When Deep Throat points out a news story about a fugitive who apparently drowned, Mulder and Scully cannot see what makes the case special but follow it up anyway. With Deep Throat's insistence, they discover evidence of a secret government project code-named Purity Control, which uses human test subjects and infects them with extraterrestrial DNA. However, the evidence and everyone who has seen it is quickly being eliminated.
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