Newly appointed Deputy Director Kersh organises a manhunt for Mulder and assigns Agent Doggett to head the team. Scully and Skinner go along with the investigation, but are warned by Kersh that they will be fired if anything is said about aliens.
Scully and Doggett continue the search for Mulder, while undeniable evidence challenges Doggett's skepticism about the paranormal.
While tackling his first X-File case, about a series of gruesome murders surrounding a bat-like creature, Doggett quickly learns that his investigative techniques are somewhat dissimilar to Scully's.
Scully evades Doggett's help in investigating a vicious murder in a remote area of Utah. She becomes trapped in the small town by a religious cult that believe a slug-like creature is the second coming of God, who needs a human host to survive.
In 1990, a little boy inexplicably disappeared from his crowded school playground and was never seen again, that is until now, 10 years later, and he hasn't aged a day since.
A prominent lawyer wakes up in jail and about to be prosecuted for his wife's murder. He has no memory of the event however, and when the days begin to regress backward towards the murder, he realises that he has been given a second chance.
Working without Scully's input, Doggett and Skinner try to avert the mysterious murder spree of a drug-induced religious cult leader, and it becomes clear that the man can enter the dreams of the people he knows and can kill them in their sleep.
When a real-estate agent is shot inside a prison cell by someone who apparently fired from the roof, Scully and Doggett track him to two exterminators, one of whom has x-ray vision.
Scully and Doggett delve into a series of bizarre deaths in a Midwestern town, but their prime suspect is pushing up daisies.
An Indian mystic, whose son died in a chemical plant accident, smuggles himself into the United States and takes his revenge on two families in suburban Washington.
Doggett comes upon an old case that Mulder kept secret from Scully, and he follows up the investigation hoping to find a possible connection to Mulder's disappearance.
Scully and Doggett must race against the clock to investigate, and fight off, a contagion lurking in the subway tunnels of Boston.
When Scully and Doggett are contacted by a man who claims his wife was murdered shortly after giving birth to an alien baby, Scully digs deeper into reports of alien fertilisation on humans and begins to question her own pregnancy and its conception.
8X14 - This is Not Happening
When Teresa Hoese, the woman Scully and Mulder met the previous spring in Oregon just before Mulder was abducted, is found in a desert, returned from tests done on her by aliens, Doggett alerts Scully that this could have something to do with Mulder and his whereabouts.
Shortly after Mulder is buried, Billy Miles is found dead, but somehow comes back to life. Skinner and Scully put all their hopes into digging up Mulder and discover that he too, is still alive. As Mulder lies in hospital without indication that he will fully recover, Krycek comes to Skinner and offers him a vaccine to the virus that has infected Mulder, but at a terrible cost.
Mulder's request for reassignment to the X-Files is denied by Kersh, who hopes that Mulder will simply quit the FBI. When a census worker is killed on the White House lawn trying to get information to the president, Mulder gets in over his head trying to discover what the man knew.
Special Agent Reyes enlists Mulder's help in investigating a supernatural killer's connection to the unsolved murder of Agent Doggett's son, Luke.
Mulder and Doggett are reluctantly thrown together to investigate several deaths on board an oil rig, and Mulder becomes convinced that the rig is carrying the black-oil alien.
Scully and Mulder rush to the rescue after Doggett and a new FBI agent get in trouble while pursuing a deadly reptilian creature.
Mulder, Doggett and Skinner try to protect Scully and her unborn child from the rampage of an alien/human hybrid.
Mulder and the other agents shield Scully and her unborn child, while delving into a possible link between her pregnancy and an extraterrestrial conspiracy.