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.
A man is chased from the Canada/US border and reportedly burned alive though his body is not found. Meanwhile, in the burned remains the FBI finds papers with the same UFO markings Scully found in Africa.
Reyes is seriously injured in a car accident and finds herself in a hospital similar to purgatory with other hospital patients suffering from serious traumas. Slowly they all begin to disappear. Meanwhile, in the real world, Doggett refuses to accept his friend's 'mortal' wounds and uses a bizarre hospital employee to both connect with Reyes in the other-world and capture a 'Dr. Death.'
After thirteen years in prison, a man named Fassl is released and cleared of murder charges when DNA evidence proves he had nothing to do with the murder of an entire family though he was present on the scene. Doggett, who made the arrest, refuses to accept Fassl's innocence and pursues the case again.