Three months after Mulder's funeral, another alien abductee's body comes back to life. Skinner exhumes Mulder hoping that he too can be revived. Skinner faces an impossible decision when Krycek offers him a vaccine that can save Mulder.
Mulder requests reassignment to the X-Files but is denied by Kersh. When a man with information about an alien invasion is killed on the White House lawn, Mulder conducts his own investigation to find further evidence of colonization.
Doggett's investigation of Kersh and the FBI isn't making him any friends, especially Brad Follmer, a new Assistant Director who has a romantic past with Reyes. Meanwhile Scully denies to tell anyone where Mulder has gone while a female super soldier is on the loose and may give Doggett the clues he needs to make his point known.
While Reyes and Skinner try to convince him otherwise, Doggett practically goes rogue for his own pursuit of the Truth. His findings, and help from the female super soldier Shannon McMahon, may lead to answers critical to the status and health of William Scully. But Knowle Rohrer is back from 'the dead' and stands in their way.
A professor/inmate in a psychiatric ward may be influencing other men to kill ritualistically. Though Doggett sees it as pure manipulation, Reyes can't help but suspect none else but the devil himself possessing the professor's body.
Agent Dogget has been shot and hospitalized. The only suspect is his partner. However, she was 14 miles away when the shooting occurred. The team sticks together to solve the case of being in two places at one time.