* ArcFatigue: Some chapters go on so long, and change perspective so frequently, and have so many hiatuses inbetween that you completely forget what happened immediately before, during, or after the scene we're watching. Given that other characters have commented on this in story, however, it can justified as Alex's way of telling long stories.
* ContinuityLockOut: It's a fairly complex plot, so it easily causes this.
* CrackPairing: Dr. Wily is apparently dating Carmen Sandiego.
* HilariousInHindsight: In [[http://www.captainsnes.com/2005/01/23/this-only-makes-it-harder-for-those-poor-kids-in-the-sweatshops/ this comic from 2005]] it was joked that Chapter 2 would end in 2008... 2009, tops. Thanks to the comic's infamous ScheduleSlip, that's ''exactly'' when it ended.
** Now Act II has been [[http://www.captainsnes.com/2009/11/22/success-retroactively/ retconned]] to have [[http://www.captainsnes.com/2004/01/23/act-iii-the-nexus-of-battle/ ended in 2004]]. Before the above comic was posted. Act III just ended, officially... despite the Final Fantasy VI cast, who started the whole 'Act III' gag, not having appeared yet.
** The Body of the Sovereign has been mentioned to rest on a moon from FFIV. Sounds like a place a godlike being [[TheAfterYears could be]].
* MemeticMutation: This strip's title, [[http://www.captainsnes.com/2012/07/04/779-memetic-mutation/ as Alex tries to remember a few memetic slogans.]]
* {{Narm}}: King Hippo's flashback of the N-Team's final battle with Mother Brain (and the events that led to it) mimics the writing style of the WesternAnimation/{{Captain N|The Gamemaster}} show. The editors of the comic were none-too-pleased.
* TearJerker: [[http://www.captainsnes.com/2011/09/16/719-melody-of-destruction/ #719]], in which the N-Team and N-Forcers watch the world of {{Crystalis}} be destroyed while the main characters of that world, realizing their fate, share one final embrace.
* WhatAnIdiot: Zeromus is the incarnation of Alex's hatred. His hatred...of coffee! Alex's real hatred is of [[spoiler:stupid people]].
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