S3E15 · Piper Maru

Piper Maru, a French salvage vessel, is exploring the Pacific Ocean. Gauthier, a member of the ship's crew, dives down into the sea and finds a sunken fighter plane from World War II. He is shocked to find a man alive in the plane's cockpit, with what looks like black oil in his eyes. When Gauthier returns to the surface, he has become possessed by the black oil.

In Washington, Walter Skinner tells Dana Scully that the FBI 's investigation into her sister 's murder has been made inactive, despite the evidence that had been recovered. Fox Mulder tells Scully about Piper Maru, which had laid anchor at the same coordinates as another ship believed to have salvaged a UFO; when Piper Maru came to port in San Diego, her crew was found suffering from radiation burns. Aboard the ship, the agents find traces of the black oil on Gauthier's diving suit. Upon viewing a video of the dive, Scully identifies the sunken plane as a P-51 Mustang. Meanwhile, Gauthier returns home and searches for something. When his wife Joan arrives, the black oil passes itself along to her.

Scully visits an old friend of her father's, Commander Christopher Johanson (Robert Clothier), seeking information about the plane. Johanson admits that he had been sent to find a sunken bomber aboard the submarine Zeus Faber and recalls how many aboard the sub suffered from radiation burns while he joined a mutiny against his commanding officer, who had succumbed to the black oil. Meanwhile, Mulder visits Gauthier's home and finds him passed out, covered in the black oil; he has no memory of his experience. Mulder finds a letter from a salvage broker and visits the broker's "secretary", Jeraldine. Mulder follows Jeraldine after her office is invaded by several armed men.

Both Mulder and Joan track Jeraldine to Hong Kong, where Mulder learns that she is a middleman selling government secrets. Mulder tracks down Jeraldine and handcuffs himself to her. Arriving at her office, he finds Alex Krycek (Nicholas Lea) waiting inside, having been selling the contents of the digital tape. Krycek escapes through a window while Jeraldine is shot by a group of men coming down the hallway. Mulder unlocks the handcuffs and escapes. Meanwhile, Joan walks down the hall and encounters the men, creating a flash that causes them all to suffer from the radiation burns.

Meanwhile, Skinner is initially confronted in a restaurant by several men, including the Gray-Haired Man, and is told not to pursue Melissa Scully's case any further. Returning to the same restaurant, Skinner sees a man, Luis Cardinal, arguing with the waitress at the counter and upon confronting him, he is shot. After Mulder catches Krycek in an airport, he tells him the tape is in a locker back in Washington and that he'll give it to him in exchange for letting him go. Mulder lets Krycek go to the bathroom, where he is confronted by Joan. As he departs the bathroom to leave with Mulder, Krycek's eyes show he is now infected with the black oil.