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Mulder: What kind of project? The autopsy of an extraterrestrial lifeform, was that part of it?
Mulder's investigation of an alien autopsy video leads to a secret project with connections to unethical experiments done by Japanese scientists during World War II. Meanwhile, Scully learns more about what happened during her alien abduction.
- Alien Autopsy: Mulder acquires videotape of one such autopsy. Scully suspects it of being a fake, only it turns out that there's some truth to it.
- Biting-the-Hand Humor: Scully dismisses an Alien Autopsy Video as "even hokier than the one they aired on the FOX network".
- Call-Back: Scully's subplot is clearly following the events set during her abduction in "Duane Barry" and "Ascension".
- Cliffhanger: Despite Scully's protests, Mulder jumps onto train 82517 as it speeds away. In the process, he drops his phone, meaning that he's alone to find out what lies in this vehicle.
- Danger Takes a Backseat: Sakurai is garroted by the Red-Haired Man as he's driven away from the Japanese consulate.
- Diplomatic Impunity: Played straight, then averted: Sakurai is released from custody despite murdering someone, only to be assassinated soon afterwards.
- Lampshade Hanging: Mulder very often drops his gun at a fight. He pulls a back-up pistol out of his ankle holster this time.Mulder: I got tired of losing my gun.
- Language Barrier: Mulder catches and arrests a Japanese spy who is part of The Conspiracy. It's not clear whether he could speak English, but he was only yelling at Mulder in Japanese. Mulder also doesn't understand his notes which frustrates him.
- Myth Arc
- Porn Stash: Scully expects Mulder to be watching porn instead of the alien autopsy video.Scully: That's not your usual brand of entertainment.
- Truth in Television: As in "Paper Clip," the episode's historical background is based on reality: Unit 731 was a Japanese army unit which experimented with chemical and biological warfare in occupied Manchuria during World War II, directly killing at least 10,000 people (mostly Chinese civilians and Allied prisoners of war) and releasing plague-infected fleas and other bioweapons into China. Shiro Zama is loosely based on Unit 731's real-life commander, Shiro Ishii, who was granted postwar immunity by the United States in exchange for his research.