Season synopsis
Contains spoilers for this season and earlier seasons.
With the X-Files closed, Scully teaches at the FBI Academy while Mulder receives surveillance work. Their separation becomes a disappearance when abductee Duane Barry takes Scully to Skyland Mountain, hoping to make the aliens choose her instead of him. Mulder arrives too late. Krycek, Mulder’s assigned partner, disappears after being exposed as a mole for the Cigarette Smoking Man. Skinner reopens the X-Files; weeks after her abduction, Scully returns in a coma, eventually recovers and rejoins Mulder. A shape-shifting Alien Bounty Hunter brings another apparent return of Samantha: she helps Mulder pursue the killer, but the woman is one of several alien clones, not proof that the real Samantha has been found. During the chase, Mulder is poisoned by the hunter’s blood and Scully saves him in the Arctic.
The season’s final investigation turns on a digital tape of classified files stolen by hacker Kenneth Soona. The information is encrypted in Navajo, and Scully takes it to New Mexico, where Albert Hosteen translates it. Mulder’s father is shot by Krycek before he can explain what he knows; Mulder’s drugged water and growing distrust of Scully nearly lead him to kill Krycek, but Scully stops him and brings him to Hosteen. Hosteen’s grandson guides Mulder to a buried boxcar filled with bodies bearing smallpox vaccination scars. The Smoking Man traces Mulder’s location through a call just before Mulder enters the boxcar. When the Smoking Man arrives, his men find no sign of Mulder inside and burn the boxcar. Mulder’s fate remains unresolved at the end of the season.