Season synopsis
Contains spoilers for this season and earlier seasons.
Mulder and Scully begin the season trying to understand the alien object found in Africa and the strange state that has left Mulder mentally overwhelmed. Scully studies the spacecraft on the Ivory Coast, while Diana Fowley secretly serves the Cigarette Smoking Man. In “Closure,” a case involving missing children draws Mulder back to Samantha’s disappearance: records and a nurse’s account show that his sister was returned after years of painful experiments, then vanished again. Mulder follows the evidence to a vision of Samantha among the children taken by the walk-ins, and accepts that she is dead.
The agents continue to investigate independent X-Files, from a New Year’s zombie outbreak with Frank Black to a case filmed as a reality show and a body that regenerates from a deadly illness. Mulder and Scully also share a New Year’s kiss, bringing their growing personal closeness into the open. Near the end of the season, reports of renewed abductions take them back to Bellefleur, Oregon, where their first case began. Scully becomes ill and is removed from the investigation; Mulder goes into the woods with Skinner and disappears in a UFO’s light alongside other abductees.
The Smoking Man sees the Oregon spacecraft as his chance to revive the conspiracy, but Krycek and Marita turn against him. Krycek pushes the wheelchair-bound man down a flight of stairs, leaving his fate uncertain. Skinner witnesses Mulder’s disappearance but cannot prevent it. When he visits Scully in hospital, she reveals that she is pregnant; the search for her missing partner is still ahead of them.