Part one Fox Mulder (
David Duchovny) and
Dana Scully (
Gillian Anderson) visit the
Area 51 installation in
Nevada after receiving a tip from an inside source concerning alien spacecraft. As they drive on the highway, the agents are surrounded by jeeps carrying soldiers led by a
Man in Black named
Morris Fletcher (
Michael McKean). A rumbling noise is heard as a
mysterious craft flies overhead and a bright light from the object passes over them. Mulder and Fletcher find that their minds have been swapped into each other's bodies, but nobody else present is aware of this. Fletcher and Scully depart, watched by the soldiers. Mulder is driven back to Area 51 along with two other Men in Black, Howard Grodin and Jeff Smoodge. After an angry telephone call from Fletcher's wife, Joanne, Mulder—still inside Fletcher's body—goes to Fletcher's home. Instead of sleeping in the bedroom, he decides to sleep downstairs in an easy chair and watch
pornography. When he is awoken by Joanne, he mumbles Scully's name. While changing his clothes, Mulder receives a call from Smoodge, who explains that the military has surveyed the wreckage of the craft from the night before, finding one of the human pilots fused into a rock but still alive. Another soldier,
Captain Robert McDonough, had switched bodies with an elderly
Hopi woman, Lana Chee, as evident from McDonough's aberrant behavior. Mulder calls Scully and tries to explain that he's the real Mulder. Scully does not believe him and asks Fletcher—in Mulder's body—to pick up and listen to the conversation. Fletcher decides they should immediately report this incident, which further confuses Scully. She goes to Mulder's apartment (where Fletcher is having a tryst with Assistant Director
Kersh's assistant) and tells him that they traced the call to a
payphone near Area 51; she suspects it is Mulder's informant. Fletcher is indifferent to this news and Scully yells at him, sensing that his behavior is very strange and his lack of concern for the
X-files is completely out of character. Deciding to investigate on her own, Scully drives through the desert towards Area 51. She stops at a burned out gas station and finds a penny and a dime fused together. Later, when Scully arrives at Fletcher's house, Mulder tries desperately to convince her of his identity. Scully remains skeptical and thinks that any information Mulder describes could be obtained in other ways. Mulder tells Scully that he will provide proof, but Fletcher, having eavesdropped on the conversation, calls his old office posing as Mulder to inform them of the source of the leak—Mulder posing as Fletcher.
Military police arrive at the appointed hour, and Mulder is dragged away, desperately pleading with Scully. Mulder asks if he would turn in an informant to the authorities in this manner as he is carried away, and Scully begins to realize that he may be telling the truth.
Part two As Mulder—in Fletcher's body—is dragged away by the soldiers, Scully begins to question whether his story about the body-swap was true. Fletcher—in Mulder's body—approaches Scully and apologizes for telling Kersh; she feigns acceptance of it. After being reprimanded, Fletcher arranges a dinner date with Scully at Mulder's apartment. Meanwhile, Mulder is confined in a cell next to the mind-switched Lana Chee. Military police take Mulder to a meeting with General Wegman, Grodin and Smoodge, who believe that Mulder-as-Fletcher was trying to defraud the
FBI, not help them. Mulder bluffs his way through the meeting, claiming that the real proof is safe and that he did not tell them about the scheme because he did not know if he could trust his colleagues, thinking any one of them could be the source of the leak. Mulder returns to Fletcher's house and tells Joanne of his true identity, but she thinks her husband must be undergoing a
mid-life crisis. At Mulder's apartment, Scully reveals to Fletcher-as-Mulder that she is on to the body-swap, demanding to know how to restore Mulder to his own body. Mulder's informant calls again, and Scully forces Fletcher to set up a meeting. Mulder, Joanne, Fletcher and Scully arrive at a bar in
Rachel, Nevada, where the informant is revealed to be Wegman. Wegman admits that he
sabotaged the UFO but maintains that he only tried to merely disable the stealth module so that Mulder could see it. Wegman gives Fletcher, who he thinks is Mulder, a
flight data recorder in a paper bag. Meanwhile, Mulder leaves and talks to Scully in the car. Later, Mulder and Fletcher meet in the bar's bathroom and argue about the flight data recorder. As they argue, Wegman enters the bathroom and discovers the two. Mulder meets with Wegman to discuss the UFO. Wegman believes that now that Fletcher knows Wegman's identity, when restored to his own body, Fletcher will turn him in. He explains that he hoped that Mulder could explain whether aliens actually exist; apparently the craft are simply given to the military without knowing where they are from or how they work. After the fiasco at the bar, Mulder and Scully meet. She sadly tells Mulder that she does not think he and Fletcher can be returned to their own bodies. However, soon after that, the warp caused by the alien craft begins to snap back and repair the natural order of the universe. Grodin, realizing that everything will be fixed naturally, gathers up Lana Chee and Captain McDonough. Scully and Fletcher arrive at Fletcher's home, and see Mulder standing by the moving truck. Joanne berates Mulder about Scully, assuming she is his lover, but he insists that he and Fletcher have swapped bodies. Fletcher goes to help Joanne move a chair and confesses that Mulder is telling the truth, telling her enough details about their past to convince her he is Fletcher. Smoodge and a group of soldiers appear at the house and detain Mulder, Fletcher, Scully and the flight data recorder in their car. Grodin explains to the group that he is restoring everything and that he reversed the body-swap between Chee and McDonough. The warp passes over them and the past few days are rewritten. Mulder and Fletcher are restored to their own bodies and returned to the moment when Fletcher's troops pulled them over on the highway. This time, no ship passes overhead and the agents leave uneventfully. Afterwards, Scully calls from FBI Headquarters to tell Mulder that they have escaped reprimand from Kersh for going to Nevada. Scully opens her desk drawer to place a file inside and finds the penny and dime that were fused together from the event at the gas station, indicating that while some things have reversed themselves, not everything has. Mulder enters his apartment and finds that Fletcher has completely reorganized and cleaned his apartment. The agents are left to puzzle over their recollection of events. ==Production==