In West Virginia, soldiers take a apparently diseased humans from an abandoned Hansen's Disease research facility and execute them. Mr. X tells Scully to look more into the implant that was removed from her neck to find more answers. On the train, the conductor says a Japanese doctor named Shiro Zama might have something to do with the quarantined railroad car. A specialist tells Scully that the implant could be replicating brain processes; also that the implant was manufactured in Japan and a shipment was sent to Zama at the West Virginia facility.
Zama is murdered by an assassin, the Red-Haired Man. Scully finds a group of survivors at the West Virginia facility, who tell her that hundreds of people have been murdered after Zama's tests there. She is captured soon after by another squad. Mulder finds that the quarantined car has been opened, and a live test subject is in a room there. The Red-Haired Man tries to kill Mulder, but ends up getting locked in the car by the conductor. Mulder holds him at gunpoint, and the Red-Haired Man tells him he's part of the NSA and a bomb has been armed on the train.
The First Elder (a compatriot of Cancer Man) tells Scully that Ishimaru was given asylum after the war. He takes Scully to another train car; she calls Mulder to tell him that tests on human subjects have been ongoing, and alien abduction is a smokescreen. She also warns that the bomb is on a timer, and thousands will die from the hemorrhagic fever the test subject is exposed to. Mulder finds the bomb, with about an hour and 40 minutes left to go, and orders the conductor to abandon the train car as far from a populated area as possible.
As the timer counts down, Mulder deduces from the Red-Haired Man's hints that the test subject is an alien-human hybrid immune to biological weapons, and that the scientists were murdered because the government doesn't want to share the breakthrough. By reviewing the tape, Scully finds the code to exit the train car and passes it on to Mulder. The Red-Haired Man knocks out Mulder and leaves the car, but is immediately killed by Mr. X. He checks out the test subject, but apparently doesn't have time to rescue it, if that was his plan. He takes Mulder away instead as the car explodes. The conspirators once again get away scot-free, and the journals Mulder took from Zama's compartment have been swapped out. The episode ends with another Japanese man working on the actual journals in the presence of Cancer Man.
The episode is presumably a reference to Unit 731, an infamous Japanese unit that experimented on human subjects to study the effects of biological weapons.
Episode Body Count
At least 25 human test subjects: executed en masse by a group of soldiers. Escalante, a survivor of the raids, says hundreds have been killed, but we don't see them and no specific number is given.
Shiro Zama: killed by the Red-Haired Man on the train.
Escalante: shot and killed by a death squad at the research facility.
The Red-Haired Man: shot by Mr. X; the railroad car explosion finishes the job if that didn't.
Test subject: presumably destroyed in the railroad car explosion. I'll put it down as an alien-human hybrid, despite its unclear status.
Humans: 28
Creatures: 0
Aliens: 1
Cumulative Body Count (59/202 episodes, 0/2 movies)
Humans: 636
Creatures: 33
Aliens: 47
Grand Total: 716
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