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. Scully , along with the Lone Gunmen, surmise that the Bounty Hunter is trying to erase all evidence of abductions and they realize that he may be going after Gibson Praise, who is now living at a school in Arizona. Agent Doggett comes to the same conclusion and his team race Scully and Skinner to the school where they find Mulder trying to kidnap Gibson.
As the search for Mulder intensifies in the Arizona desert, Gibson Praise leads Scully to believe that she is truly closer to her target. Meanwhile AD Kersh informs Agent 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.
Having been kidnapped for ten years, a little boy mysteriously reappears in the same place as he was kidnapped but somehow has not aged one bit while he was away. Doggett and Scully investigate the case further but find that something is definitely not right with the child.
A prominent lawyer wakes to find himself in jail and about to be prosecuted for the murder of his wife. He has no memory of this event however, and when the days begin to regress backward towards the murder, he realizes 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.
Doggett and Scully encounter a dead man who is still living – only somewhat changed. What they discover is a man made of metal, exacting vengeance on those he believes created him and caused this horrid process to happen to him.
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 decides to investigate it in more detail hoping to somehow find a link to Mulder’s possible whereabouts. But while investigating Doggett stumbles onto something that he never knew about Mulder but all of this information comes at a high price when his life is put in danger.
Scully and Doggett race to investigate a string of bizarre deaths in the tunnels of the Boston subway system linked to a mysterious killer. But the agents are put under pressure when they have to investigate the case on a short deadline because the subway is going to be reopened.
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, the woman Scully & Mulder met the previous spring in Oregon just before Mulder was abducted, is found in a desert, returned from testing 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 very dead but somehow comes back to life. Skinner and Scully put all their hopes into digging up Mulder and discovering that he too, is still alive. As Mulder lies in hospital without indication that he is going to fully recover, Krycek comes to Skinner and offers him a vaccine to the virus that has infected Mulder – but the cost of the vaccine is that Skinner has to kill Scully’s unborn child.
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.
Agent Reyes enlists Mulder’s help investigating a killer’s connection to the unsolved murder of Doggett’s son. They investigate but find no connection, Reyes continues to believe that a thread of evil is linking all the murders together.
After Agent Mulder goes beyond his jurisdiction to shine light on a possible X-file, Doggett is assigned to investigate the mysterious disappearance of two men aboard an oil rig. Once he arrives, he finds Mulder has taken it upon himself to start his own investigation. Mulder soon becomes convinced that the rig is drilling the black oil. Doggett and Mulder must attempt to stop the spread of the alien virus while avoiding the infected crew.
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 but when they disappear as well, Mulder, despite having left the FBI, heads out to search for them.
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. They encounter Billy Miles, who has been changed into an alien replicant after his recent abduction and is attempting to erase evidence of the tests; part of the Syndicate’s conspiracy with an alien race. When a woman helping Scully out at home is found to be a part of the conspiracy, the agents, along with Monica Reyes and Alex Krycek, know they must protect Scully and her baby from Billy Miles and get her out of the city
With otherworldly factions in pursuit, Mulder and the agents race to safeguard the birth of Scully’s child. Scully and Reyes take refuge in an abandoned town where Doggett grew up. Meanwhile Doggett and Skinner have the final showdown with Alex Krycek and continue to fight off the replicants but how successful will they be?