Assuming Mulder is dead, the FBI strips Scully of her credentials for withholding information about the missing computer disk.
Reunited, Mulder and Scully secretly continue the investigation; they learn the truth about Mulder's parents and discover Skinner's true colors.
After deaths are attributed to lightning, Mulder and Scully determine a teen who survived a lightning strike may be the murderer.
3X04 - Clyde Bruckman's Final Repose
While tracking a serial killer of fortunetellers, Mulder meets a man (Peter Boyle) he believes to be a genuine psychic.
An inmate's final vow prompts the agents to investigate a mysterious death which occurred after the man's execution.
When a lonely woman on a blind date is brutally murdered, Mulder links her case to earlier disappearances of women looking for love in the wrong places. Scully's analysis reveals strange discrepancies in the victim's weight and body composition - somehow the killer removed all the fat from the corpse - and he is still out there looking for another victim.
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 takes out his personal frustrations on his commanding officers.
Mulder seeks the help of a woman whom, 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.
The agents uncover more information in the government's attempt to hide the truth about extraterrestrial life when Mulder discovers a video of an alleged alien autopsy.
The agents' investigation into the government's knowledge of extraterrestrial life puts them in danger; Scully is forced to trust a mysterious man.
Mulder and Scully must protect a child from a serial killer with a penchant for murdering those claiming to suffer from religious wounds.
3X12 - War of the coprophages
Mulder and Scully visit a town under attack from killer cockroaches. When Mulder discovers they are not insects but highly-complex robots, he questions whether they come from this planet at all.
The agents visit a small town to investigate a series of bizarre deaths that coincide with strange astrological phenomena.
The agents assist Mulder's former mentor with a case involving a serial killer who claims to be possessed by a demonic force.
The divers from a French salvage ship fall prey to a bizarre illness after working on a mysterious wreckage from World War II.
Mulder uncovers more clues about a government cover-up involving an alien entity and a sunken World War II aircraft. Scully pursues the man who murdered her sister.
Mulder battles a manipulator when the agents are assigned to a case involving a man seemingly capable of bending people to his will.
An ancient artifact brought from South America to Boston triggers a series of deaths. With David Duchovny and Gillian Anderson.
The agents investigate the mysterious deaths of Chinese immigrants whose bodies were missing various internal organs.
3X20 - Jose Chung's From Outer Space
Mulder and Scully must sort through differing stories while investigating a couple who claim to have been abducted by aliens.
Mulder and Scully learn more about Director Skinner's personal life as they work to unravel a conspiracy and clear him of murder.
The agents investigate deaths and disappearances near a lake where small-town residents revive stories about a legendary killer sea-serpent.
The agents uncover a government mind-control experiment thrust upon unsuspecting citizens via their television sets.
The agents search for a man who possesses strange powers, and uncover a dangerous secret from Mulder's past that could expose the truth about alien existence.