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.

Mulder and Scully are reunited once again. However, Scully's sister, Melissa, has been shot by the men responsible for Mulder's father's death. A meeting with the Lone Gunmen sends the agents to find Victor Klemper, a patriated Nazi who worked for the same group Mulder's father worked for. Meanwhile, Skinner negotiates with the Cigarette Smoking Man for Mulder and Scully's lives.

A series of bizarre lightning deaths brings Mulder and Scully to a midwestern town. They suspect a teenage boy who has recently survived a lightning strike and believe to be capable of creating lightning on his own will.

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.

A prisoner on death row vows to return and kill all those people who have wronged him. When a mysterious death occurs after his execution, Mulder and Scully are called in to investigate.

Mulder and Scully track a serial killer with a bizarre and horrifying M.O. Although, they have not much leads in the case, they discover the victims have several things in common.

Mulder and Scully are called in to investigate a man with several injuries that were reportedly to be cause by suicide attempts at a military hospital. Later, they discover a quadruple amputee who has gained the power of Astral Projection and is taking revenge his commanding officers.

The kidnapping of a girl from her room sends Mulder down to the scene of the crime when he learns that a woman across town suffered a nosebleed as well as uttered the exact same words that the kidnapped girl did. While Scully and the other agent in charge investigate the facts of the case, Mulder tries to find evidence that the woman and the girl have a psychic connection.

Mulder and Scully unravel another government's conspiracy to hide the truth about extraterrestrial life when Mulder uncovers a video of an alien autopsy.

Mulder is able to enter the train that is carrying the boxcar that he had been looking for. Inside the train, he begins to look for anyone connected with the contents of the car. Meanwhile, Scully confronts Mulder’s source. She wants answers and he tells her that the implant that she had taken out of her neck will provide her with more information than he could ever give her.

Mulder and Scully is assigned to protect a little boy who is displaying inexplicable wounds of religious significance from a killer.

Mulder investigates a series of deaths that are linked to killer cockroaches. He discovered a government agricultural agency may be behind a secret experiment involving insects.

Mulder and Scully are called in to investigate a series of bizarre deaths in a small town where Mulder discovers those deaths seem to be linked with a strange astrological phenomena.

Mulder and Scully, together with Mulder's former mentor are investigating a case involving a serial killer who claims to be possessed by a demonic force. Although, the suspect is apprehended but the murders continue.

A French salvage operation in the Pacific Ocean goes awry when the team discovers an unknown entity. Mulder soon learns that the entire team has been relocated to the San Diego Naval Hospital for treatment of radiation burns. Their ship, the Piper Maru, had been searching for something in the exact same area that the vessel, the Talapus, had been seen on satellite photos a few months back (Nisei). Mulder and Scully head to the west coast to investigate.

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 challenged by a man who seems to have the ability to control others. He leaves clues for Mulder and Scully to follow as he sets up his contest of wills.

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.

Mulder and Scully are called in to San Francisco's Chinatown to investigate the deaths of several Chinese men found to be missing vital internal organs.

When a couple claims to have been abducted by aliens, Mulder and Scully try to find out the truth, but it turns out to be impossible task since everyone has a different version of the story.

Skinner is accused of murder. Mulder and Scully tried to help him clear his name. Both of them discovered that there is a conspiracy to prevent them from finding out the truth.

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.

A hostage situation in a fast food restaurant is quickly resolved when a man steps forward to heal the gunshot wound of one of the victims. When police arrive, the man who healed the victim is interviewed by the detective in charge, but the man then mysteriously vanishes.