S3E16 · Apocrypha

On August 19, 1953, a burned crewman talks to three government agents about his experience on the submarine Zeus Faber, completing the story told in the previous episode. He explains that he and other crew members were locked in with their captain, who was infected by the black oil. After being knocked out from behind, the black oil leaves the captain's body and exits via a grate into the sea. It is revealed that Bill Mulder and the Smoking Man are two of the agents who are interviewing the crewman.

In the present, Fox Mulder and Alex Krycek return to the United States, but are run off the road by another vehicle. The assailants attempt to apprehend Krycek, but are severely injured when he emits a flashing light. The Smoking Man sees their bodies and orders their destruction. Mulder, who was knocked unconscious in the crash, awakens in the hospital. Dana Scully tells Mulder about Walter Skinner 's condition, and says that an analysis of saliva has identified his shooter as the same person who killed her sister Melissa.

The Syndicate meets to discuss the events surrounding Piper Maru and realizes someone is leaking information. Meanwhile, Skinner tells Scully that he recognizes his shooter as the man who was with Krycek when the digital tape was stolen from him. Mulder believes that the black oil is a medium used by an alien to transfer from body to body, and that Krycek is currently occupied by it. Mulder and the Lone Gunmen use Krycek's key to recover the digital tape from a locker at an ice rink, but Mulder finds the case empty. Krycek, possessed by the black oil, returns the tape to the Smoking Man in exchange for the location of the recovered UFO.

As Luis Cardinal is identified as Skinner's shooter, the Syndicate admonishes the Smoking Man for moving the UFO to a new location. By rubbing a pencil over the envelope containing the tape case, Mulder finds a phone number which connects him to the Syndicate's office. Mulder speaks to the Well-Manicured Man, who offers to meet with him. The Well-Manicured Man tells Mulder that a UFO was sunk during World War II and that a cover story of a sunken atomic bomb was used to cover up its attempted recovery. He reveals that anyone can be gotten to, causing Mulder to ask Scully to check on Skinner.

Scully accompanies Skinner as he is being transported in an ambulance. When Cardinal attempts to break in, she tracks him down and arrests him. Cardinal tells her that Krycek is headed to an abandoned missile silo in North Dakota. There, the agents are captured by the Smoking Man's men and are escorted away. Deep inside, Krycek sits atop the UFO as the alien, suspended in the black oil inside of Krycek's body, is painfully excreted out of Krycek's facial orifices, which then seeps into the ship. Skinner recovers and returns to work. Mulder sees Scully at Melissa's grave, explaining that Cardinal was found dead in his cell. Meanwhile, Krycek is trapped within the silo, banging on the door in an attempt to be let out.