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                           Im feeding the chip impulses...it means the neural network is storing information

At the Hansen's Disease Research Facility soldiers arrive and round up a group of deformed patients. As one of the patients hides in the woods and watches, the patients are all gunned down by the troops. Scully loses contact with partner Mulder, who has lost his cell phone as he jumps aboard a moving train. Scully questions X on how to help him, who tells her to research the chip that was put in her neck, that it will help her learn more about the train and who killed her sister. Mulder enters the train and talks to the Conductor, trying to get access to Dr. Zama. Inside Zama's compartment they find journals hand written in Japanese. Scully sees Agent Pendrall who tells her that the chip replicates the brain's memory function and can enable someone to know a person's every thoughts. By researching it, Pendrall has effectively destroyed the chip. They find the manufacturer of the chip to be Dr. Zama from a disease research facility in West Virginia.

On the train the Red-Haired Man kills Dr. Zama. His body is later found by Mulder and the Conductor. Scully heads to the Hansen's Disease Research Facility where she finds a group of diseased patients hiding underneath the floor. One of the patients, Escalante tells her that lepers and other deformed people had been experimented upon here by Dr. Zama. He tells her that the medical staff left and that soldiers arrived, killing all except those who hid. Escalante shows her a large pit filled with their corpses. Immediately afterwards a helicopter and troops arrive, capturing Scully. Mulder heads to the quarantined train car, seeing the alien-like person inside. The Red Haired Man gets the jump on him, causing the Conductor to lock the two of them in the car. The Red Haired Man claims to be an agent of the National Security Agency and that there is a bomb on the train.

Scully meets the First Elder, who tells her that the people here were part of an inhuman experiment by Zama. The First Elder permits Scully to contact Mulder by calling the Red Haired Man's cell phone. Scully tells Mulder that alien abductions, including her own, had nothing to do with aliens but rather were experiments conducted by people like Zama, with the alien abduction theory simply being a smoke screen. Scully believes that the quarantined patient in the car has hemorrhagic fever and thousands will die of it if the car explodes. Mulder finds the bomb in the ceiling, with approximately 100 minutes remaining.

Mulder tells the Conductor to disconnect the car from the rest of the train in an unpopulated area. The Red Haired Man tells Mulder that the quarantined patient is a weapon, someone with immunity to biological warfare. Zama tried to sneak it out of the country, but the government would rather see it destroyed than let the Japanese steal the technology. Mulder believes that the patient is an alien human hybrid. Scully tries to contact Senator Matheson and X but has no luck. By watching Mulder's alien autopsy video she figures out the car's exit code, which she tells to Mulder. As Mulder opens the door out of the train he is knocked unconscious by the Red Haired Man. As the Red Haired Man is about to leave, he is shot to death by X, who enters the car and saves Mulder, leaving just as the car explodes.

A week later Mulder finds himself unable to get any information on the car. Scully returns the journal he found on the car, but Mulder realizes that it is a rewritten substitute. Meanwhile the real journal is translated in a shadowy room as the Cigarette Smoking Man watches

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