The sixth season of the science fiction television series The X-Files commenced airing on the Fox network in the United States on November 8, 1998, concluding on the same channel on May 16, 1999, and consisted of twenty-two episodes. The season continued from the 1998 feature film and focused heavily on FBI federal agents Fox Mulder and Dana Scully's separation from the X-Files Division and the demise of the Syndicate—a "shadow government" group attempting to cover up the existence of extraterrestrials—in the two-part episode "Two Fathers" and "One Son".

Fox William Mulder is a fictional FBI Special Agent and the secondary protagonist of the Fox science fiction-supernatural television series The X-Files, played by David Duchovny. Mulder's peers dismiss his many theories on extraterrestrial or paranormal activity as those of a conspiracy theorist and supernaturalist; however, his skeptical but supportive partner, Special Agent Dana Scully, often finds them to be unexpectedly correct. He and Scully work in the X-Files office, concerned with unsolved FBI cases that are often revealed to be supernatural or extraterrestrial in nature. Mulder was a main character for the first seven seasons, but was limited to a recurring character for the following two seasons. He returns as a main character for the tenth and eleventh seasons.