With Mulder presumed dead, Scully returns to Washington for a hearing on her conduct. Unfortunately for her, she is summarily suspended without pay or benefits from the FBI. In New Mexico, the Navajo who led Mulder to the alien bodies in the boxcar find the agent buried under rocks in the quarry near the car. It is there that they begin the ceremony to heal Mulder.
A.D. Skinner and Scully are at a standoff when Mulder bursts in and discovers that Skinner has the digital tape. Reunited, Mulder and Scully travel to a secret vault inside a mine and find an elaborate filing system of medical records which reveals that Mulder's sister may not have been the first choice for abduction. Meanwhile, Skinner deals with the Cigarette-Smoking Man for their safety.
Mulder and Scully investigate a series of human and cattle deaths by lightning and are led to a teenage boy who is the only survivor out of five people recently hit by lightning strikes.
In the course of tracking a serial killer preying upon fortune tellers, Mulder and Scully enlist the help of a man whom Mulder believes to have the ability to foresee how people will die. The psychic has visions of Mulder's death.
Nobody takes much notice when a death row inmate vows on the electric chair to come back from the dead and kill five men who have wronged him during his time in prison, until a guard is mysteriously murdered in the former inmate's cell.
A man with a genetic abnormality who must prey on overweight women in order to suck the fatty tissue from their bodies, begins to meet his victims through internet chat rooms.
After a suicide attempt and multiple murders at a military hospital, Mulder and Scully meet a quadruple amputee who has gained the power of astral projection and is taking out his personal frustrations on his commanding officers.
Mulder seeks the help of a woman who he believes has a special connection with a young girl who has recently been kidnapped by the same man who held her captive many years earlier.
An investigation into a video of an alien autopsy puts Mulder and Scully in the middle of a conspiracy involving WWII Japanese scientists brought to America to continue their experiments which may shed light on Scully's abduction.
Mulder is trapped inside a train car which contains a suspected alien-human hybrid and also a bomb, while Scully pursues the truth about her abduction and the mystery behind the implant in her neck.
Mulder and Scully swap roles as they pursue a man killing priests that claim to have the wounds of Christ. The agents find and must protect a young boy who may be a real stigmatic. While Scully's faith draws her close to the boy, Mulder is convinced of another explanation.
Widespread panic is caused in a small community after numerous deaths are linked to killer cockroaches, and a government agricultural agency is discovered to have set up a secret experiment involving insects.
A rare planetary alignment causes strange behavior in the residents of a small town, but particularly in two teenage girls who were born at the exact same moment on that date.
A serial killer is captured after a three year manhunt, and he claims an evil spirit is responsible for the crimes. When the killings continue as he sits in jail, Mulder's battle with a former colleague gets more heated when he suggests that something more paranormal may be involved.
A French salvage ship searching for a lost WWII fighter plane unknowingly surfaces an alien which appears in the form of black oil and has the ability to jump hosts. Mulder heads to Hong Kong to investigate the salvage broker who sold the information to the French and he encounters Krycek, who has been selling information from the MJ documents. As Mulder prepares to take Krycek back to the US, the alien makes its way to Hong Kong and takes control of Krycek.
Mulder returns from Hong Kong with Krychek in tow. However, they are attacked by unknown agents and Krychek manages to escape while Mulder finds himself in a hospital. Meanwhile, Skinner is also admitted to the hospital suffering from a gunshot wound fired by a man who is working for the group that wants Scully's sister's murder investigation to end.
Mulder and Scully are asked to help in a case involving Robert Patrick Modell, a murderer possessing the psychic ability to force his will onto people. Due to a brain tumor that is slowly killing him, he is searching for a "worthy adversary" and forces Mulder into a battle of mind over matter.
An ancient artifact, which was brought to Boston from an excavation site in South America, is believed to be linked to a series of deaths. While Scully suspects that political terrorism may be behind the murders, Mulder believes in something far more sinister.
The deaths of several Chinese men found to be missing vital internal organs that were removed prior to death leads Mulder and Scully to a deadly Chinatown lottery where men wager their body parts for a chance to win a cash jackpot.
A alien abduction of two teenagers with endless versions of the same story prompts a science-fiction novelist to to write a book about the incident; however, nobody involved with the investigation can tell him the full story with any accuracy.
During a one-night-stand in the midst of his divorce, A.D. Skinner becomes a murder suspect, and Mulder and Scully return the many favors that he has done for them by analyzing evidence that someone doesn't want uncovered to prove his innocence.
Mulder and Scully are called in to investigate a series of mysterious deaths and disappearances near a lake in a small town. Mulder believes that the local legend about a lake monster may be all too real.
Mulder receives a tip from an unknown informant about a case where a man murdered several people, believing that all of them were the same person. In the same neighborhood several weeks prior, a similar murder scenario had occurred. When Mulder and Scully investigate the man's house, they find hundreds of VHS tapes with cable program recorded on them.
Mulder and Scully search for a mysterious man with the power to heal. His actions risk exposing the existence of aliens on Earth, while a confrontation between Mrs. Mulder and the Cigarette-Smoking Man leads Mulder to the discovery of the only weapon which can kill the aliens.