Their first case takes them to Oregon to investigate the unsolved murders of several high school classmates, whom `Spooky' Mulder believes have been experimented on by aliens.
Mulder and Scully return to the town of their first X-Files investigation where a UFO has crashed in the forest. CSM arranges for Krycek to be released from prison in order for him to make contact with the aliens and begin rebuilding the `Project', while Scully's health appears to be taking a turn.
Shortly after Mulder is buried, Billy Miles is found dead, but somehow comes back to life. Skinner and Scully put all their hopes into digging up Mulder and discover that he too, is still alive. As Mulder lies in hospital without indication that he will fully recover, Krycek comes to Skinner and offers him a vaccine to the virus that has infected Mulder, but at a terrible cost.
Mulder and the other agents shield Scully and her unborn child, while delving into a possible link between her pregnancy and an extraterrestrial conspiracy.
Mulder, Doggett and Skinner try to protect Scully and her unborn child from the rampage of an alien/human hybrid.
