In flashback, government agents (among them a young William Mulder and The Cigarette-Smoking Man) visit the deathbed of a radiation-scarred crewman who served aboard the submarine Zeus Faber (see episode 3X15). The man insists the Navy tricked the submarine's crew into believing that their mission was to recover an atomic bomb from a sunken aircraft. But he believes the real purpose of the mission was to guard an alien entity living on the ocean floor-a life-form that invaded the sub and killed crewmen with deadly radiation. The Cigarette-Smoking Man assures the crewman that the government will make the truth public.

In present day Washington, Scully visits Skinner at a hospital. Skinner, semi-conscious, reveals that he recognized his assailant. Fearing further attacks, Scully assigns guards posted outside his hospital room.

Meanwhile, Mulder orders Krycek to drive him to the location where the digital tape is stored. During the journey, another vehicle deliberately slams into Mulder's car, forcing it off the road. Mulder is injured in the crash and loses consciousness. Armed men confront Krycek and demand the tape. Moments later, a blinding white light emanates from Krycek's body and strobes the armed men.

Scully visits Mulder at the hospital where he's recuperating from injuries suffered in the car crash. Scully produces lab tests that prove Skinner's assailant and her sister's killer are one and the same. Later, the agents examine the diver's suit Gauthier wore during the salvage mission. Mulder points out a layer of diesel oil covering the suit. He believes the oil is a medium used by an extraterrestrial to jump from host to host. Krycek, Mulder postulates, is the alien's latest host.

With the aid of the Lone Gunmen, Mulder recovers a package believed to contain the digital tape. The tape case inside the package is empty, but faint pen strokes on the outside of the paper package reveal the Well-Manicured Man's phone number. Mulder arranges a face-to-face meeting in hopes of learning Krycek's location. Krycek, meanwhile, gives the tape to the Cigarette-Smoking Man. During their meeting, the Well-Manicured Man tells Mulder a UFO was downed by American pilots over the Pacific Ocean during the second World War. Missions to salvage the craft failed because of intense radiation. Mulder realizes that the Well-Manicured Man doesn't know where Krycek is.

Meanwhile, Scully guards Skinner as he is transported to another hospital. The Hispanic Man, Luis Cardinal, attempts to gain access to the ambulance. But Scully surprises him and a chase ensues. Cardinal is struck by an automobile and falls into an alleyway. Terrified Scully will shoot him, he reveals that Krycek is headed for an abandoned missile site outside Bismarck, North Dakota.

The agents gain access to the site, but the Cigarette-Smoking Man has them taken into custody before they can search all the silos. Later, we see Krycek inside a silo where an alien spacecraft is hidden. The entity exits Krycek's body, leaving him entombed within the silo.

Later, Mulder tells Scully that Luis Cardinal was found dead inside his jail cell-a death made to look like a suicide.