Mulder goes to the Bermuda Triangle when he learns that the Queen Anne, a British luxury liner which disappeared during WWII, has re-appeared in the middle of the Sargasso Sea. Mulder's boat is wrecked and after floating in the water, he is hauled aboard the ship which has just been hijacked by the Nazis searching for the man who will build the atom bomb.
Mulder tries to convince the crew that they have traveled into the future but evidence further suggests that it is he, who is back in the past.

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 realises 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 it's wake and Mulder and his alter ego must race to put themselves back where they belong.