The mythology of The X-Files, sometimes referred to as its "mytharc" by the show's staff and fans, follows the quest of FBI Special Agents Fox Mulder (David Duchovny), a believer in supernatural phenomena, and Dana Scully (Gillian Anderson), his skeptical partner. Their boss, FBI Assistant Director Walter Skinner, was also often involved. Beginning with season 8, another skeptic named John Doggett, and Monica Reyes, a believer like Mulder, were also introduced. The overarching story, which spans events as early as the 1940s, is built around a government conspiracy to hide the truth about alien existence and their doomsday plan. Not all episodes advanced the mythology plot, but the ones that did were often set up by Mulder or Scully via an opening monologue.
Most mythological elements in The X-Files relate to extraterrestrial beings, referred to by the writers as "Colonists", whose primary goal is to colonize Earth. Late in the series, this was revealed to have been planned for the year 2012.
This list of mythology episodes is taken from official sources, The X-Files Mythology range of DVDs and the book The Complete X-Files: Behind the Series, the Myths and the Movies. Differences between the DVDs and the book are shown, where appropriate.
FBI Special Agent Fox Mulder (David Duchovny) has made a name for himself, "Spooky Mulder," working on X-Files—unexplained cases which may be paranormal in origin. He is appointed a partner in these investigations—Dana Scully (Gillian Anderson)—with his superiors hoping that she will be able to debunk and discredit his work. Their first case together is the investigation of possible abductions in Oregon, which falters when their evidence is destroyed in a fire. A later case, involving the disappearance of a United States Air Force test pilot, sees the introduction of secretive informant Deep Throat (Jerry Hardin), who continues to provide the agents sensitive information. This help is supplemented by conspiracy theorist group The Lone Gunmen, who are contacted for help in a further abduction case. Deep Throat is killed, however, when he helps the agents uncover details of a government human cloning program, and the X-Files unit is closed shortly thereafter.