A salvage vessel, the Piper Maru, sets anchor on the wind-scarred waters of the Pacific Ocean. The French-speaking crew lowers a diver, Gauthier, into the briny depths. Gauthier discovers the wreckage of a World War II fighter on the ocean floor, creating jubilation amongst his comrades. But as Gauthier peers into the glass canopy of the aircraft, he sees a living World War II pilot, his eyes covered with a thick black membrane, trapped inside. Certain he is hallucinating, Gauthier goes topside. But as the crew works to unsuit him, they fail to notice a black filmy membrane that now covers Gauthier's eyes.
     Meanwhile, back in Washington, Skinner informs Scully that due of a lack of new leads or evidence, local police have made her sister's murder investigation inactive.
     Afterward, Scully joins Mulder in his office. Mulder shows her evidence that the Piper Maru had been anchored in the exact location where the crew of the Talapus (see episode 3X09) had performed scavenger work. He also reveals that everyone aboard the Piper Maru, except Gauthier, suffered acute radiation burns. The agents travel to a ship yard and examine the vessel. Mulder notices an oily film covering the diving suit. He and Scully find videotape footage of Gauthier's dive-and see the remains of the submerged World War II aircraft.
     Gauthier, meanwhile, returns to San Francisco and begins ransacking a home office. His American wife, Joan, catches him in the act. Gauthier attacks Joan, and shortly thereafter, her eyes become covered by the same black film. Mulder finds Gauthier semi-conscious, on the kitchen floor. Gauthier only remembers events up to his discovery of the sunken aircraft, and nothing about the ransacked apartment. Mulder also finds a letter linking J. Kallenchuk Salvage Brokers to the mystery.
     Scully tracks down an old neighbor and World War II vet, Commander Christopher Johansen, hoping he can shed some light on the sunken aircraft. As luck would have it, Johansen reveals he was aboard the submarine Zeus Faber during its mission to locate the plane-which had been transporting an atomic bomb during the war. He recounts how the sub crew took ill during the mission, and how he took over command when the Captain became irrational.
     Mulder follows Geraldine Kallenchuk (who runs the salvage brokerage) to Hong Kong. He handcuffs himself to Geraldine and breaks into her office. Alex Krycek suddenly appears and gets the drop on Mulder. He forces Geraldine (still handcuffed to Mulder) into the hallway and dead bolts the door, separating the two. Gunshots suddenly ring out, and Geraldine is killed. Krycek escapes through a window. Mulder unlocks the handcuffs and he, too, flees the scene.
     Meanwhile, back in the U.S., Skinner is shot in the stomach by the Hispanic Man (Luis Cardinal) (who, with Krycek, killed Scully's sister). Skinner is rushed to the hospital.
     Mulder surprises Krycek at the Hong Kong airport. He punches him in the face, pulls a gun and demands the return of the digital tape. Krycek gives the agent a key, claiming the tape is kept inside a locker back in Washington. Mulder allows him to use a rest room so he can remove the blood from his face. But Joan Gauthier suddenly appears inside the men's room and attacks Krycek. The filmy black substance transfers from Gauthier to Krycek.