Season synopsis
Contains spoilers for this season and earlier seasons.
Dana Scully wakes in hospital after a seizure and realizes that the epidemic and UFO that ended Season 10 were a vision of a possible future. Her seizures continue, and dreams lead her and Fox Mulder to an abandoned ferry where two teenage girls have attacked each other while seeing a monster called Ghouli. Their investigation reaches Jackson Van De Kamp, William, the son Scully placed for adoption: he has used his powers to make the girls see Ghouli, and he fakes his death before escaping Department of Defense agents. DNA confirms his connection to Scully, but the parents lose him again. Meanwhile, the Cigarette Smoking Man and a rival faction led by Mr. Y and Erika Price seek the young man for their competing plans. The Smoking Man tells Walter Skinner that he artificially impregnated Scully and claims William as his son; Mulder continues to identify himself as William's father.
The search runs alongside new X-Files: a presumed-dead friend reaches Mulder through a corporate digital afterlife; deaths linked to doppelgangers bring the agents to telepathic twins; and other cases involve an artificial intelligence, a suspected occult attack on a child and stolen organs. Mulder and Scully's relationship also changes as they become intimate again. In the finale, William uses his powers to appear as Mulder, and the Smoking Man shoots him, believing he has killed his rival. The real Mulder then shoots the Smoking Man and throws him into the water; the episode leaves his survival uncertain. Bubbles rise and William emerges alive in the final image, suggesting his powers have made him exceptionally difficult to kill. Scully tells Mulder she is pregnant with his child, closing the season on another unexpected pregnancy while William's future and the Smoking Man's fate remain unresolved.