Mulder is missing and assumed dead . . . although Scully experiences a vision in which he is still alive. Yet even as they are reunited, each must deal with an additional personal loss, tragedies that ultimately serve to strengthen their connection to each other. And they soon find themselves depending on that strength as familiar foes resurface and preconceived notions are shattered.
Scully finds her career with the FBI in jeopardy as Mulder is still missing and the Cigarette-Smoking Man is pursuing the stolen files. The Navajo elders find Mulder's body in a cave and perform an ancient ceremony to call the spirit back to the empty vessel.
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 midst of a psychic sideshow while on a murder case, Mulder and Scully enlist the help of a man who may have a true psychic ability to foresee how people will die to help the agents catch a man killing fortune tellers.
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 pursues Krycek (unaware of the alien that has taken over his body) to get back the DAT tape containing the MJ documents. Meanwhile, the shooting of A.D. Skinner uncovers evidence that could lead Scully to her sister's murderer.
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.
The unearthing of an ancient Ecuadorian Amaru urn and its removal to America despite protests leads to a series of deaths linked to a shaman spirit released by the urn.
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 investigate a series of disappearances and attacks around a lake where Mulder believes that the local legend about a lake monster may be all too real.
After a man kills three people and his wife because he mistook them for a ruthless middle eastern dictator, Mulder and Scully discover a test involving mind control using television signals that make people's worst fears become real in any form.
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.