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 killer murders Reyes and mortally wounds Doggett...in another dimension. Reyes, under investigation for a nearly killed Doggett realizes the killer can shift dimensions to fill out his disgusting fantasies.
Doggett and Reyes are unsure whether a boy intentionally or unintentionally can control the habits of flies; during the investigation Scully acquires a new 'partner'.
Doggett wakes up in Mexico and can't remember his name or what he is doing there. His only clues are small flashbacks of a child (his son) and two mysterious marks on his head.
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.
Reyes, Doggett, and Scully are pulled into a bizarre serial murder case involving the number '3', numerology on a whole, and an eccentric man who likes to play checkers.
Reyes and Doggett, with the aid of a young Mulder-worshiping FBI agent, investigate a father who is exhibiting bizarre behavior regarding his son who he has kept hidden from the outside world.
A Frank Black-esque cadet in Scully's class directs Doggett to a current murder case that may have something to do with a case that went unsolved 9 years prior...the murder of his young son.
Mulder's return leads to his being tried before a military tribunal that seeks to justify and prove the very existence of an alien conspiracy -- and the X-Files.