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The X-files are generally any unexplained and paranormal cases outside the FBI Bureau mainstream. The first X-file, initiated by J. Edgar Hoover himself, stemmed from a series of murders in and around the northwest in 1946, in which the victims were shredded and devoured by a half-animal/half-man suspect. Although the beast was cornered and killed by police that year, similar murders also occurred in 1954, 1959, 1964, 1978 and 1994.

After several years of being closed cases, they were finally reopened in 1991 by an agent named Fox Mulder. Through the course of the show, the X-files has revolved around the investigations of Mulder and his partner, Special Agent Dana Scully.

In 1973, Mulder's sister, Samantha, was taken from the Mulder home by a force Mulder often refers to as extraterrestrial. Mulder then went on to discover the X-files, which is designated as any file unsolved or paranormal in nature. His work in the X-files was largely an attempt to find his sister, and the acquisition of these files was frowned upon by the FBI. As a deterrent, the Bureau assigned Agent Dana Scully to debunk Mulder's theories--hoping her scientific explanations would provide her superiors reason to close the X-files. However, Scully was (and is) rarely able to explain the phenomena, and her comraderie with Agent Mulder has enhanced her loyalty to the X-files through the years.

The mythology of The X-files is the backstory of the tale, and roughly one-third of the episodes target the "mytharc" in some way. The mytharc itself deals with the storyline of the Syndicate, a group of government men associated with a conspiracy of alien/human hybrids, alien abductions and evidence that extraterrestrials might have created all mankind.

At the end of season 8, the baton was passed from the partnership of Fox Mulder and Dana Scully to John Doggett and Monica Reyes. Although they continue to investigate the mythology of The X-files, Doggett and Reyes still have little knowledge and involvement in the conspiracy to conceal the alien Colonization of Earth.

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