Principal Settings: Perkey, West Virginia; Washington, D.C.
If you look at the Japanese book that Mulder flips through early in the episode (In the doctors train compartment), you will notice that all the pages contain the exact same text.
The covert army guys in this episode and in "731" seem extremely unprofessional. First off in 731 they dump over a hundred corpses in a ditch about 30 ft long and 20 feet across and they don't even try to fill a gaping hole in an open field leaving Scully to bear witness to it. Even though they were on guard it was still a serious risk. In this episode they chase after Mulder and Scully for five minutes before without shooting them as soon as they saw them especially with an unidentified flying object in one of the nearby silos unless they received word from the CSM not to.
If you watch closely you can see that Mulder runs the keycard through the door scanner the wrong way, scanning nothing but plastic.
Mulder: We're both gonna die in here. The difference is, I'm gonna die quickly. As an employee of the National Security Agency you should know that a gunshot wound to the stomach is probably the most painful and the slowest way to die. But I'm not a very good shot. And when I miss, I tend to miss low.
Hitman: You have no idea what you're dealing with here.
Mulder: Yeah, well maybe you should have filled me in before you tried to kill me!
Hitman: I work for the National Security Agency.
Mulder: The NSA? Since when did they start issuing you guys piano wire instead of guns?
1st Elder: The ruler of the world is no longer the country with the bravest soldiers, but the greatest scientists.
Scully: Well done, Agent Pendrell. Keep up the good work.
Agent Pendrell: Hey, thanks. Keep it up yourself!
(Scully looks at him strangely before leaving)
Agent Pendrell: Keep it up yourself... what a doof...
Mulder: You know what I think. I think you're a liar. I don't think you work for the NSA. And I don't think there's a bomb on this train.
Red Haired Man: You're choosing a hell of a way to find out.
Scully: Don't you see Mulder, you're doing their work for them. You're chasing aliens that aren't there, helping them to create the story that covers the shameful truth. And what they can't cover, they apologize for. Apology has become policy.
Mulder: Maybe. Maybe you're right Scully. But I don't need an apology for the lies. I don't care about the fictions they create to cover their crimes. I want them held accountable for what did happen. I want them to apologize for the truth.
Two cameras were destroyed while filming this episode.
The name of the doctor, Takeo Ishimaru, and his alias, Shiro Zama, is an amalgamation of the name of the real head of Unit 731, Dr. Shiro Ishi.
This episode's tagline is changed to 'Apology is Policy', spoken by Scully shortly before the end: "... and what they can't cover, they apologize for. Apology has become policy."
The title refers to Unit 731 which was a special unit of Japanese scientists who experimented on prisoners of war during WWII. Like their Nazi counterparts, these scientist may have been given refuge in the USA to continue their experiments.