Mulder receives word that a Navy destroyer, the U.S.S. Ardent, vanished in the waters of the North Atlantic. Eighteen survivors were rescued by a Canadian trawler, but only one, Lieutenant Richard Harper, survived the mysterious incident. Harper is admitted to the Bethesda Naval Hospital in Maryland where he is placed under tight security. Scully gains access to Harper's room. She is surprised to discover that Harper-who is twenty-eight years old-looks like an elderly man. Mulder is unsurprised when he hears the news. He tells Scully about the Philadelphia Experiment, a top secret World War II project in which the United States government attempted to render battleships invisible to radar. Not long afterward, the U.S.S. Eldridge vanished from a Philadelphia Navy Yard only to reappear minutes later, hundreds of miles away in Norfolk, Virginia. Mulder believes these events are linked to the Roswell Incident. He theorizes that government physicists may have been trying to manipulate worm holes on earth.

The agents travel to Norway in search of answers. They meet Henry Trondheim, the captain of a trawler called the Zeal. Trondheim tells of a legendary stone that Greenlanders believe is an evil god. Mulder and Scully hire Trondheim to navigate the treacherous waters and dense fog. Despite Trondheim's best efforts, his ship collides with the Ardent. The agents, accompanied by Trondheim and his first mate, Halvorsen, board the Ardent and discover dead bodies covered with a strange substance. Suddenly, the sound of an engine fills the air. The foursome race onto the ship's deck, only to see the Zeal disappearing into the fog. They realize they are stranded. A man's scream shatters the ghostly quiet. Mulder, Scully and Trondheim race to the ship's mess hall, where they discover Halvorsen's dead body. More sounds in the galley lead them to a faltering old man, Captain Phillip Barclay, who claims that his ship encountered a strange light that stopped time itself. A short time later, Barclay dies. A man named Olafssen, a pirate whaler and wanted criminal, suddenly rushes Trondheim. Mulder draws his weapon and orders Olafssen to stop. A fight ensues between Trondheim and Olafssen, but Mulder convinces Trondheim that Olafssen, who has not aged, may hold clues to the mystery. The Ardent's log describes how four Norwegian sailors were rescued after their ship had sunk. This leads Trondheim to speculate that Olafssen's men stole his boat and left their leader stranded. Not long afterward, Scully, Mulder and Trondheim begin aging rapidly.

Scully develops a theory about the sudden aging. If the ship had drifted close to another massive metallic source-such as a meteorite-the resulting electromagnetic energy could excite free radicals, the elements suspected of causing aging. The agents suspect that drinking desalinized water from the ship's tanks is the source of the aging. If Olafssen drank recycled sewage water, which does not come from the sea, it may have kept him from contracting the illness. While the agents are away, Olafssen tells Trondheim that drinking the recycled water will save his life. Trondheim kills Olafssen and begins drinking from a toilet bowl. With the recycled water supply dwindling rapidly, tension begins to escalate. Trondheim locks himself in the ship's sewage hold and backflushes all the water into a single tank. With no water left to drink, Scully improvises by combining sardine juice, limes, and the water from a snowglobe. Before either can consume the precious drinking water, the ship's outer hull gives way and the vessel is flooded. Trondheim is overcome by the freezing water and drowns. Scully and Mulder are rescued by helicopter, and doctors are able to revive them.