After Mulder’s disappearance, Scully returns to FBI headquarters to find Special Agent John Doggett heading up a FBI manhunt for her partner. Knowing that type of search will prove futile, Scully and Skinner turn to the Lone Gunmen in hopes of uncovering information about additional UFO activity around the time of Mulder’s disappearance. Although such information leads them to Gibson Praise, the man with Gibson, a man who appears to be Mulder, is in fact an alien bounty hunter. Finally realizing that Mulder will not be found so easily, Agent Doggett is officially assigned to the X-Files. Now, after all she has been through with Mulder, it is Scully who is “the believer” and who must find a way to work with “the skeptic,” John Doggett.
Newly appointed Deputy Director Kersh organizes a manhunt for Mulder and assigns Agent John 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.
As the search for Mulder intensifies in the Arizona desert, Gibson Praise leads Scully to believe that she is truly closer to her target. Kersh informs Doggett that he has been assigned as Mulder's successor on the X-Files.
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, and she is 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 young boy inexplicably disappeared from his crowded school playground and was never seen again until now—ten years later—and he hasn't aged a day.
A prominent lawyer wakes to find himself in jail and about to be prosecuted for the murder of his wife. However, he has no memory of the event and, when the days begin to regress towards the murder, he realizes he has been given a second chance.
Working without Scully's input, Doggett and Skinner try to stop 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.
A man whose blood is rapidly changing into metal alloy enacts revenge on those who caused his condition.
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, D.C.
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 fertilization on humans—and begins to question her own pregnancy and its conception.
When Teresa Hoese (who Scully and Mulder met just before Mulder's abduction) is found in a desert after enduring alien testing, Doggett alerts Scully that this could have something to do with Mulder and his whereabouts. Skinner joins them and they travel to the hospital where Teresa is clinging to life by a thread—and Scully soon realizes this is exactly what's going on with Mulder.
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.
Mulder's request for reassignment to the X-Files is denied by Kersh, who hopes that he 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 Doggett's son.
Mulder and Doggett are reluctantly thrown together to investigate several deaths aboard an oil rig, and Mulder becomes convinced that the rig is really carrying the black oil alien.
While Scully takes maternity leave, Doggett is partnered with a young agent who is fascinated with the X-Files and has followed Mulder and Scully's careers. She and Doggett investigate the death of an old man and the disappearance of his son.
Mulder and Doggett join forces to investigate the arson attack on a genetics lab where one of the doctors suspected of experimenting with alien impregnation is killed.
Mulder, Doggett and Skinner attempt to fight off the alien replicants, and they find a connection to the conspiracy that leads into the FBI. Reyes and Scully head to a remote farm to safeguard the birth of Scully's child.