Mulder goes to the Bermuda Triangle when he learns that the Queen Anne, a British luxury liner which disappeared during WWII, has reappeared 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.

While being detained near the famed "Dreamland" Area 51, a strange craft flies overhead and Mulder swaps bodies with an Area 51 "Man-in-Black". While the other agent has fun in Mulder's body, Mulder himself finds it difficult to fit into someone else's life, especially a shadowy one. Mulder contacts Scully about the body swap and tries to get her the flight data recorder from the UFO test flight, but his alter ego uses Mulder's FBI persona to have him arrested.