Shortly after Mulder is buried, Billy Miles is found very dead but somehow comes back to life. Skinner and Scully put all their hopes into digging up Mulder and discovering that he too, is still alive. As Mulder lies in hospital without indication that he is going to fully recover, Krycek comes to Skinner and offers him a vaccine to the virus that has infected Mulder - but the cost of the vaccine is that Skinner has to kill Scully's unborn child.

Agent Reyes enlists Mulder's help investigating a killer's connection to the unsolved murder of Doggett's son. They investigate but find no connection, Reyes continues to believe that a thread of evil is linking all the murders together.