Season synopsis
Contains spoilers for this season and earlier seasons.
With Mulder in hiding, Scully returns to teaching at the FBI Academy and Monica Reyes becomes John Doggett’s partner in the X-Files office. A case tied to a dead Environmental Protection Agency official leads Doggett and Walter Skinner to a reclamation plant, a secret naval experiment and Doggett’s former Marine colleague Shannon McMahon, who identifies herself as a super-soldier. The agents find that the program is connected to Scully’s son, William. Scully, Doggett and Reyes also face a dangerous UFO cult that targets the child and briefly kidnaps him.
Scully and Reyes eventually recover William, but a scarred intruder later enters the X-Files office. Doggett suspects he is Mulder, and a DNA match seems to support that possibility. Scully remains unconvinced: he is Jeffrey Spender, Mulder’s half-brother, who injects William with a substance that removes the child’s unusual powers. Scully decides that she cannot keep him safe and arranges his adoption. Meanwhile, Doggett gets a resolution to his son Luke’s murder, and the Lone Gunmen die stopping a bioterrorist attack in “Jump the Shark.”
In the two-part finale, Mulder resurfaces at a military base and is arrested after Knowle Rohrer apparently dies in a fight. At his tribunal, Scully’s examination proves the body is not Rohrer, but the court rejects her evidence and sentences Mulder to death. Kersh changes sides, helping Scully, Doggett, Reyes and Skinner break him out. Mulder and Scully reach New Mexico and find the Smoking Man alive at the Anasazi ruins; helicopters destroy the site, but Mulder and Scully escape. They become fugitives, while Doggett and Reyes find the X-Files office shut down.