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.
Mulder is thrown in jail at the Area 51 compound but is released when it is discovered that the flight data recorder he stole was a fake. Scully comes to her senses and realizes that the Mulder she sees isn't who he really is and heads back to Nevada to help the real Mulder. Meanwhile, the mechanism that caused the body swap is rapidly snapping back, undoing everything in its wake, and Mulder and his alter ego must race to put themselves back where they belong.