Seven years after their first case there, the agents are called back to Oregon by Billy Miles, a boy and abductee they helped during their prior visit. In a desperate attempt to restart the Project, the CSM hopes to retrieve a UFO from the Oregon town. Mulder and Scully hope to find it first. In Season 7's final moments, Mulder is abducted along with a host of other people; Scully learns that she's pregnant, and Alex Krycek and Marita Covarrubias finally kill the CSM ... or so it appears.
But even without the CSM, the Colonists continue their plot, using their Alien Bounty Hunters to create new human-alien replacements known as super-soldiers. As Scully and Skinner search for Mulder with help from new X-Files assignee Special Agent John Doggett, what appears to be Mulder's corpse returns to Earth. After months, Mulder is resurrected as his body begins the alien replacement process triggered by his previous exposure to the black oil virus. Thankfully, Scully finds a way to save him and prevent his transformation into a super-solider.
Billy Miles, on the other hand, becomes a super-soldier and begins erasing all evidence of the Project, making sure the Colonists' mission remains a secret. Mulder, Scully, Doggett, Skinner, and newcomer Monica Reyes fight back to expose the conspiracy, killing Krycek in the process. As Scully gives birth to her son, multiple super-soldiers gather to watch in awe, believing the child to be something more...
