Season synopsis
Contains spoilers for this season and earlier seasons.
After Mulder vanishes in Oregon, Scully searches for him while distrusting John Doggett, the FBI agent leading the official task force. Once the hunt fails, Doggett is assigned to the X-Files and becomes Scully’s partner. The investigation brings Monica Reyes, an agent who specializes in ritualistic crime, into their circle. Cases continue as Scully tries to keep working while pregnant, but the larger mystery keeps returning to the abductees and the secret forces moving through the Bureau.
The search takes a devastating turn when Mulder’s apparently dead body is found in the forest. He is buried, but evidence from returned abductee Billy Miles gives Scully hope; Mulder revives after three months and recovers under her care. He briefly investigates again, but is subsequently dismissed from the FBI after an oil-platform investigation, with Doggett remaining in charge. During Scully’s maternity leave, Doggett is paired with inexperienced agent Leyla Harrison for one case, while Reyes and Skinner stay involved.
Krycek warns Skinner to kill Scully’s unborn child and later helps Mulder, Doggett and Skinner uncover the super-soldier conspiracy. Billy Miles and other people have been replaced by nearly indestructible alien agents, who believe Scully’s baby may threaten them. As Miles closes in, Reyes gets Scully to an abandoned town in Georgia. Skinner shoots Krycek dead; Scully gives birth to William, who appears ordinary, and the surrounding soldiers withdraw without explanation. Mulder arrives, and the season ends with the family together while Doggett and Reyes return to the FBI.