Thrown out of his dingy by a ferocious storm in the Sargasso Sea, Mulder is fished out the ocean by hostile sailors. When he regains his wits, he realizes he's boarded the "Queen Anne", an English luxury liner that disappeared in the 1930s during World War II.
Brought before the ship's captain Yip Harburgh, Mulder tries to explain that the war is over and that the boat has been caught in some kind of time warp called the Devil's Triangle for the past 50 years. But he captain and crew have very different feelings, as the reality of the moment tells us that the liner has been captured by Nazi soldiers. The Nazis believe that the boat is carrying "Thor's Hammer", which they assume to be an atom bomb. When Mulder accidentally reveals that "Thor's Hammer" is the scientist who can make an atom bomb, the Nazis steer a path for Germany, hoping to use the atom bomb technology to win the war.
The atom bomb scientist on board is traveling with a woman who looks identical to Scully. Mulder enlists the aid of the Scully look-alike, telling her she must turn the ship around and save the future. If she doesn't, the Germans will win the war, and ultimately, Mulder and Scully will not exist. The Scully look-alike is confused, but Mulder is in a hurry, he's got to get back to his own history. Realizing he may never get another chance, he gives the Scully look-alike a deep kiss, for which she repays him with a "special" kiss of her own - a right hook to his chin. Mulder jumps overboard.
Meantime, the Lone Gunmen approach Scully at FBI headquarters and inform her of Mulder's disappearance. She enlists the help of Skinner to get information from the Navy's satellite tracking system to find the missing ship.
Racing to the spot where Mulder disappeared, the Gunmen and Scully find the ship and rescue Mulder. At the hospital, the Lone Gunmen, Scully and Skinner visit Mulder. He tries to explain all that happened, but they downplay it as a dream. They all wish him a speedy recovery and leave. It is then that Mulder feels a bruise on his face given to him by one of the Nazis. And he realizes it wasn't a dream after all.