- Awesome Music: And this is, fellow tropers, how you compose epic score for a movie. Mark Snow's expanding on the theme and the varying main titles sound divine.
- Fandom-Enraging Misconception: For a while, calling this movie 'The X-Files: Fight the Future'! "Fight the Future" was originally a slogan, placed where a subtitle would go and thus mistaken for one. Some people could get really bent out of shape if you did this, but (1) it really did look like a subtitle, (2) the movie's gotta be called something, and (3) "I Want To Believe" really is the next movie's subtitle and it's in the same place in the logo as the words "Fight the Future" were on the first. By now, it's officially a subtitle; even The Powers That Be finally conceded.
- Harsher in Hindsight: The Well-Manicured Man expounds on the power and breadth of FEMA, telling Mulder that when the alien virus is released into the general public, the government will declare a state of emergency and the country will come under FEMA's control. He goes as far to say that FEMA is the "secret government" and that it has the power to operate outside of federal control during a natural disaster. This may have had some weight in 1998, but following FEMA's relegation from an independent agency to part of DHS after 9/11 and its widely criticized lack of response to Hurricane Katrina in 2005, these comments seem... odd upon rewatch.
- Narm: The immortal line "We will take that with which he cannot live without." Don't think about it too hard.
- One-Scene Wonder: Armin Mueller-Stahl's brief performance as Conrad Strughold, international head of the Syndicate, was well-received by fans. But the character never reappeared, nor was mentioned again.
- Shipping: The scene in Mulder's hallway is really intense, especially that Almost Kiss. So close! Damn you, you stupid bee!
YMMV / The X-Files: Fight the Future