With great interest, Mulder views a mail order videotape which purportedly contains an actual alien autopsy. The footage shows a team of Japanese surgeons performing the procedure. The tape suddenly ends when a group of armed soldiers storms the operating room. Mulder and Scully trace the tape's origin to a video piracy operation in Allentown, Pennsylvania. When the agents arrive at the scene, they find a man's body with a pillowcase tied over its head. Mulder chase a Japanese man fleeing the scene and takes him into custody. Skinner reveals that the suspect, Kazuo Takeo, is a high-ranking government official from the Japanese diplomatic corps.
     Mulder searches Takeo's leather satchel, uncovering satellite photos and a list of names containing members of the Mutual UFO Network. Mulder learns that the satellite photos contain images of a salvage ship named the Talapus, which spent months searching for a Japanese sub sunk during World War II. The ship made port in Newport News, Virginia, leading to speculation that perhaps the Talapus found something other than the downed sub.
     The list of Mutual UFO Network members leads the agents to a Lottie Holloway and Penny Northern. They tell Scully that she is one of them. Confused, Scully insists she is conducting an FBI investigation into the murder of Steve Zinnzser (the man found with the pillow case over his head). The women tell the agents that Zinnzser was a member of their group. They also describe their experiences in a "bright white place," triggering Scully's partial memory of what transpired during her disappearance. The women display small pieces of metal which were surgically removed from the back of their necks. They bring Scully to the hospital, where another member of their group, Betsy Hagopian, is dying of an undiagnosed cancer ailment. Penny claims everyone who was abducted will die in the same fashion.
     Meanwhile, Mulder travels to Virginia where he discovers the Talapus hidden between much larger vessels. Nearby, Mulder discovers an airplane hangar that houses a large circular object-which the Talapus must have dredged from the bottom of the sea.
     Skinner tells Mulder that the Japanese diplomat was found murdered. Later, Mulder visits Senator Matheson, who requests the return of the satellite photographs. Mulder believes that doing so would entangle him in the murder investigation. In a cryptic gesture, Matheson gives Mulder a list containing the names of four murdered Japanese scientists.
     Scully and Mulder meet at FBI headquarters. Mulder displays a photograph of Japanese medical officers taken during World War II. Four of the men are the same surgeons found murdered the previous day. Mulder suspects that the scientists were trying to create a human-alien hybrid, a continuation of their work, and similar work done by the Nazis, during the war. He suspects that the U.S. government may be behind the murders. Mulder also shows Scully a photo of train cars which he believes are part of the government's secret railroad, one of which was used to carry out the alien autopsy.
     Mulder travels to Quinnimont, West Virginia, where he discovers train cars from the satellite photos. As Mulder prepares to jump onto one of the moving cars, Scully contacts him on his cellular phone. She passes on information, given to her by X, that his life is in great danger. Nonetheless, Mulder jumps on top of the train car.