In this continuation of the previous episode... X tells Scully that the metallic implant (which was surgically removed from the back of her neck) is the key to all the answers she's been searching for.
     Meanwhile, Mulder--who clings precariously to the top of a train bound for Canada--makes his way to safety and climbs aboard one of the cars. He the car which is quarantined and cut off from the rest of the train. With assistance from the train's conductor, Mulder searches for Dr. Shiro Zama, whom he suspects is behind the experiments. But the Red-Haired Man (an assassin who murdered the Japanese diplomat in the previous episode), kills Zama and hides his body inside a lavoratory.
     With the aid of Agent Pendrell, Scully learns that the implant collects information and artificially replicates a person's mental processes. Pendrell discovers the name of the chip's manufacturer, a Japanese firm, and traces a delivery to Dr. Zama at Hansen's Disease Research Facility in Virginia. Scully attempts to contact Mulder by cellular phone to relay the information, but unknown to her, Mulder dropped the device when he jumped onto the train. Scully drives to the research facility, where she encounters Escalante, a hideously deformed man. Escalante explains that the facility was once a leper colony, but the staff, including Zama, fled when death squads arrived to kill the patients. Escalante was being treated for leprosy, but hundreds of other patients were interned at the camp with symptoms that resembled the disease. The creatures were kept apart from the patients and apparently tortured.
     Meanwhile, Mulder finds Zama's body inside the lavoratory. He is suddenly attacked by the Red-Haired Man. With the conductor's help, Mulder overcomes him. The Red-Haired Man claims the quarantined car is rigged with an explosive device, which was installed by Zama in case he could not escape to Canada with his creature. Mulder and his captive are unable to leave the quarantined car out of fear that opening the door without the proper access code might detonate the bomb.
     Scully is captured by soldiers and brought before an Elder, a member of the Syndicate. He explains how Zama-a brilliant scientist whose real name is Ishimaru-was hidden in the U.S. after World War II so he could continue his experiments. But Ishimaru kept his discoveries secret, unwilling to share his knowledge with the government that had granted him asylum. Scully and the Elder dial the Red-Haired Man's cellular number and contact Mulder. Scully believes the creature aboard the train isn't an alien being after all. She's convinced Ishimaru used the railroad to conduct secret radiation tests on lepers, the homeless, and the insane. As proof, she reminds Mulder about the President's public apology for secret radiation tests that were conducted on innocent people until 1974. Only those tests never ended.
     The quarantined car is uncoupled from the train in an isolated area. Mulder questions the Red-Haired Man about the creature, and theorizes how Zama developed a human-alien hybrid with super immunity, capable of withstanding the effects of atomic and biological weapons.
     Scully reviews the alien autopsy tape and realizes Zama was caught on video punching in the proper code to open the door of the quarantine car. She phones Mulder with the code. But before he can exit the car, Mulder is attacked by the Red-Haired Man. X arrives, shoots the Red-Haired Man, and rescues Mulder moments before the train car explodes.