- Crowning Moment of Awesome/Crowning Moment of Funny: David Duchovny's uncredited cameo in the season finale, and the ensuing conversation between Mulder and Jimmy.
- Fanon Discontinuity: "Jump the Shark" was not well-recieved, and at least a small portion of the fanbase claims Fletcher was lying through his teeth when it came to the Gunmen's fates.
- Word of God confirms that Fletcher did just that and the Gunmen are alive and well.
- The IDW comic, meant to be a canon continuation of the show, further confirms this. Heck, they got to star in a major event crossover!
- "Funny Aneurysm" Moment (Just watch the pilot.)
- Harsher in Hindsight: The pilot episode, which aired March 4th, 2001.
Byers Sr:The Cold War's over, John. But with no clear enemy to stockpile against, the arms market's flat. But bring down a fully loaded 727 into the middle of New York City and you'll find a dozen tinpot dictators all over the world just clamoring to take responsibility, and begging to be smart-bombed.
- Fast forward six months to September 11, 2001...
- Narm / Special Effects Failure: Tom Braidwood (Frohike) and Bruce Harwood (Byers) are standing on a fully visible Scully Box in the promotional shot used for the cover of the special edition comic book. It... somewhat detracts from the dramatic dignity of the shot.