* CrowningMomentOfAwesome[=/=]CrowningMomentOfFunny: David Duchovny's uncredited cameo in the season finale, and the ensuing conversation between [[DeadpanSnarker Mulder]] and [[BookDumb Jimmy]].
** The moment in the dance contest episode where Frohike bails out on the guys and isn't seen until near the end - turns out the short, homely fellow was once "El Lobo," the tango champion of Miami and had to go find his old dance partner.
* FanonDiscontinuity: "Jump the Shark" was ''not'' well-received, and at least a small portion of the fanbase claims Fletcher was [[UnreliableNarrator lying through his teeth]] when it came to the Gunmen's fates.
** WordOfGod 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!
* FunnyAneurysmMoment (Just watch the pilot.)
* HarsherInHindsight: The pilot episode, which aired March 4th, 2001.
-->'''Byers Sr:'''''[[TheGreatPoliticsMessUp The Cold War's over]], John. But with [[WhyWeAreBummedCommunismFell no clear enemy to stockpile against]], [[WarForFunAndProfit the arms market's flat]]. But [[FalseFlagOperation bring down a fully loaded 727 into the middle of New York City]] and you'll find a dozen [[AcceptableTargets tinpot dictators]] all over the world just [[TooDumbToLive clamoring to take responsibility]], and [[WhatAnIdiot begging]] to be [[RoaringRampageOfRevenge smart-bombed]].''
** Fast forward '''''six months''''' to September 11, 2001...
* {{Narm}} / SpecialEffectsFailure: Tom Braidwood (Frohike) and Bruce Harwood (Byers) are standing on a fully visible ScullyBox in the promotional shot used for the cover of the special edition comic book. It... somewhat detracts from the dramatic dignity of the shot. Seeing as the Gunmen were comic relief, this may have been deliberate.

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