An anonymous tip finally brings Mulder and Scully to the mecca of all UFO lore - Area 51. But when the agents witness the flight of a mysterious craft, their lives are profoundly - and perhaps irrevocably - altered.

Mulder drags Scully deep in the Nevada desert to meet a "source" who supposedly works at Area 51 and is going to give Mulder proof positive of the government's experimentation with alien technology. Unfortunately, before they can rendez-vous with the informant, they are stopped by other Area 51 officials who tell them they must turn around. As Scully tries to haul Mulder back into the car, a UFO flies overhead. It emits a massive heat ripple which switches the personalities of Mulder and Morris Fletcher, one of the Area 51 officials. Unbeknownst to anyone other than Mulder and Morris, Morris (who now inhabits Mulder's body) climbs back into the car with Scully, leaving Mulder (who is now in Morris' body) with the Area 51 goons.

Entrenched behind the walls of the mecca of UFO lore, Mulder tries to untangle the mess he's found himself in. Morris, on the other hand, is just happy to be given this new life as a single FBI agent; he doesn't lift one finger to try to reverse the situation.

Mulder tries to prove to Scully that he is not Morris, though Scully is skeptical at best. He tells her he will give her scientific proof via a flight data recorder which was recovered from another plane that crashed during test flights at Area 51. Unfortunately, Morris (aka Mulder) gets wind of Mulder's plan and informs A.D. Kersh. Kersh then orders Scully to set a trap for Mulder. The Area 51 police arrive and capture Mulder. And as Scully watches the MPs drag off this man who looks like Morris Fletcher, but claims to be Mulder, she wonders if there may be any truth to the odd turn of events.