731 (The X-Files) - Plot

Plot

In West Virginia, a team of soldiers arrives at an abandoned leprosy research compound, rounding up most of the patients. One patient, Escalante, hides beneath a trapdoor during the arrival and follows the group to a secluded field nearby. He watches as the soldiers shoot the other patients—including apparent alien-human hybrids—into a mass grave.

Fox Mulder loses his cell phone after jumping on top of the moving train, losing contact with Dana Scully. When questioned by Scully, X tells her to analyze her implant, saying that it will give her answers about the train and Melissa's murder. Meanwhile, Mulder enters the train and finds that the secret railcar is quarantined and protected by a security system. He searches for Zama, enlisting the train conductor for help. In Zama's compartment, they find hand-written journals in Japanese. However, elsewhere on the train, the Red-Haired Man intercepts and strangles Zama.

Scully sees Pendrell, who tells her that the implant contains highly advanced technology that can replicate the brain's memory functions and enable someone to know a person's very thoughts. The manufacturer of the chip was Zama, who created the implant at the West Virginia compound. Scully travels there, meeting a group of deformed patients who have eluded the "death squads." Escalante tells her that the patients were experimented on by Zama, who departed long ago; since then, the death squads have set out to massacre them. Escalante shows her the mass grave, but is killed when soldiers arrive to capture Scully. She is brought before the First Elder.

Mulder returns to the railcar, seeing its door ajar; an alien-human test subject is locked in a room inside. The Red-Haired Man attacks Mulder, causing the conductor to lock them both in the car. The Red-Haired Man claims to work for the NSA, and that a bomb in the car was triggered after he gained entry with Zama's pass code. Mulder doesn't believe him, but is called by Scully on the Red-Haired Man's cell phone. Scully—who is with the First Elder in a similar railcar—tells Mulder that unwitting subjects, including herself, were operated on by Zama in the secret railway, with the alien abduction theory used as a smokescreen. She also confirms that a bomb is in the car, and believes that the quarantined patient is infected with hemorrhagic fever. She fears that thousands will die from the disease if the car explodes. Mulder finds the bomb in the ceiling.

He has the car disconnected from the rest of the train on a remote rail siding. Mulder then questions the Red-Haired Man, who says that the quarantined patient is immune to biological warfare. Zama had tried to sneak the patient out of the country, but the government would rather see it destroyed than let their research fall into Japanese hands; the Red-Haired Man was sent to kill them both. Mulder, however, believes that the patient is an alien-human hybrid.

With the bomb approaching detonation time, Scully is able to determine the railway car's exit code. Mulder successfully unlocks the door, but he is knocked unconscious by the Red-Haired Man. As the Red-Haired Man is about to leave, X appears and shoots him. Realizing that the bomb is about to explode and that there is not enough time to both save Mulder and secure the quarantined patient, X decides to save Mulder. After briefly looking through a small window to see the alien-human hybrid, X exits while carrying the still unconscious Mulder shortly before the bomb explodes.

After recovering from his injuries, Mulder attempts to find information on the railway car, but he is unable to do so. 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.