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, A.D. 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.

In 1990 a little 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. 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 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 she begins to question her own pregnancy and its conception.

When Teresa Hoese (the woman Scully and Mulder met the previous spring in Oregon just before Mulder was abducted) 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 realizes that this is exactly what's going on with Mulder.

Shortly after Mulder is buried, Billy Miles is found very dead, but he 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 the 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.

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 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, but when they disappear as well Mulder 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. 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.

Mulder, Doggett and Skinner attempt to fight off the alien replicants, and they find a connection to the conspiracy that leads into the FBI while Reyes and Scully head to a remote farm to safeguard the birth of Scully's child.

Agent Doggett investigates the death of an EPA official after his car is forced off a bridge by a woman he picked up. He asks for assistance on the case from Scully, who has returned to her teaching position at the FBI Academy in Quantico.

Doggett catches up with Shannon McMahon, the woman who the EPA official picked up. She claims to be a super soldier and that the people she has killed were poisoning the water supply, and she wants Doggett to expose the truth.

Doggett and Reyes investigate the murder of a couple in West Virginia that has all the signs of a satanic ritual killing. They link the murder to a doctor who is incarcerated in a mental institute, and Doggett becomes convinced that the doctor is orchestrating the crimes from within the hospital.

During a stakeout of murderer Irwin Lukesh, Doggett sees Reyes attacked by Lukesh, but then we see Reyes and Doggett in her apartment, apparently both fine. Elsewhere at the same time, Doggett is shot and Lukesh identifies Reyes as the shooter. While Reyes is asked for her badge and gun by A.D. Follmer, and Doggett lies in hospital near death, the conflicting circumstances of the stakeout and Doggett's shooting do not add up and it becomes clear that Lukesh possesses the power to switch between parallel universes and alter the events in each.

When a stunt on a local cable reality show goes horribly wrong resulting in a man's death, Doggett and Reyes investigate. But when flies pour out of the victims eye sockets, they find themselves relying on Scully's expertise and ask her to join the investigation.

Scully is approached by a couple who claim their baby has the same abilities as William and have information about the super soldier program; however, they will only talk to Mulder, believing him the only person who can make the connections and uncover the truth. Scully is forced into an awkward situation when she has to decide whether to put Mulder's life in more danger even though she desperately wants to see him.

Scully and Reyes join forces to try and find Doggett when he goes missing. Doggett has his own problems, having woken up in jail in Mexico suffering from amnesia. With no knowledge of who he is, Doggett is befriended by a local who soon has him working smuggling illegal immigrants across the border.

Agent Reyes takes the lead while investigating an X-file case, surrounding a man found skinned alive after having visions of seeing other people appearing skinned alive. Reyes calls on Scully's expertise to help on the investigation, which pays off when Scully finds a link to a case from 1960.

When pieces of the spaceship beached in Africa resurface, the conspiracy within the FBI attempts to hide the information from the X-Files, especially the one person for whom the pieces have a special significance - Scully. When Doggett and Reyes discover that Scully and her child have been put in great danger, they race to protect her and William from the evil forces pursuing him, and Scully is forced to take drastic measures to protect her child.

Scully is anxious to recover William from his kidnappers and takes matters into her own hands when the FBI's attempts to assist in the investigation are less than helpful. With the help of the Lone Gunmen, Scully discovers terrifying information about her child's captors, and is once again forced to confront the mystery regarding the sinister interest in her son.

After a car accident, Reyes finds herself in a very gray area, while Doggett desperately denies doctors' diagnoses about his partner, who witnesses a strange disappearance.

Scully, Doggett and Reyes investigate an old case that Doggett worked on as a cop in Brooklyn, dubbed "The Screwdriver Killer". They try to determine whether the man who was convicted and has just been released from prison was actually the man responsible for the murders.

When Reyes uses numerology to connect the murders of several women to an obsessed serial killer, she and Scully become trapped with a mysterious checker-playing man who may or may not be the killer.

Agent Harrison talks Doggett and Reyes into investigating a boy's claim that monsters killed his mother, who was officially determined to have stabbed herself repeatedly.

The agents ask the Lone Gunmen to help find their friendly foe Yves Adele Harlow after former Area 51 Man-In-Black Morris Fletcher claims she is one of the super-soldiers.

Doggett catches someone in the X-files office trying to steal documents pertaining to Mulder's sister. The intruder is a severely scarred man who blames his disfigurement on Government conspirators. He claims the source of that information - and, in fact, the one who helped him gain entry - is Mulder. Although he refuses to divulge the missing agent's whereabouts, the mystery man has enough knowledge of the X-files and its history to lead Doggett to suspect that he just might be Mulder himself. Scully's fears for the safety of her son are elevated when he is injected with an unknown substance. With the mystery surrounding William becoming even darker, Scully must allow herself to send him away for his own safety.

When an FBI cadet with amazing profiling skills approaches Doggett, Reyes, and Scully with a lead on a suspect in a series of recent murders, he claims the same killer is responsible for the death of Doggett's son. The agents find themselves wondering if his knowledge of the deaths is because of his obsession with the cases he has studied at Quantico, or if he is in some way involved in the murders.

Doggett and Reyes investigate a murder outside the house that the original Brady Bunch series was filmed in. The house is owned by a man named Oliver who is obsessed with the show and has rigged the house into a series of traps and changing appearances to look like the Brady house.

After not knowing Fox Mulder's whereabouts for the last year, A.D. Skinner and Agent Scully learn he's being held for the murder of a military man he couldn't possibly have killed: Knowle Rohrer, one of the government's secret super-soldiers. With Skinner acting as Mulder's defense, people who Mulder has dealt with during his last nine years as an FBI agent testify on his behalf. But the military tribunal isn't interested in the truth.

When an unexpected person comes to Mulder's rescue, Mulder refuses to slip north over the border to safety. Instead, he heads southwest to the Anasazi ruins of New Mexico seeking a mysterious wise man who the Indians call "The Keeper of the Truth".