The exploits of FBI Special Agents Fox Mulder and Dana Scully who investigate X-Files: marginalized, unsolved cases involving paranormal phenomena. Mulder believes in the existence of aliens and the paranormal while Scully, a skeptic, is assigned to make scientific analyses of Mulder's discoveries that debunk Mulder's work and thus return him to mainstream cases.
Scully finds her career with the FBI in jeopardy as Mulder is still missing and the Cigarette Smoking Man is pursuing the stolen files. The Navajo elders find Mulder's body in a cave and perform an ancient ceremony to call the spirit back to the empty vessel.