Aware his presence only puts Scully and William in jeopardy Mulder once again disappears — but at least this time it is his own choice. A frustrated Agent Doggett tries to find Mulder so he can proceed with his investigation against Deputy Director Kersh, but Scully and Skinner finally convince him to drop his case. Yet even as Scully helps Agent Doggett and Agent Reyes on some of their cases she realizes William is still in danger. When she learns a religious cult wants her son dead she turns to the Lone Gunmen. But even they cannot prevent William from being kidnapped, a fact which forces Scully to make a painful decision. Yet even in her darkest hour she receives word that Mulder has been found — and is being held in a military brig for the murder of a man who cannot die.
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 solider 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".