* CrowningMomentOfAwesome[=/=]CrowningMomentOfFunny: David Duchovny's uncredited cameo in the season finale, and the ensuing conversation between [[DeadpanSnarker Mulder]] and [[BookDumb Jimmy]].
* FanonDiscontinuity: "Jump the Shark" was ''not'' well-recieved, 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.
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