* HilariousInHindsight: ''R!'' has a minor theme of older strategies becoming outdated... and then the following started happening in the game itself...
** The PowerCreep to ensure mass swarming seems to be an eerie prediction of how the game would shift from the Synchro era onwards, with weak monsters being used en-masse in combos designed to build up larger and larger fields. Hell, Yako's usage of Summoner Monk seems to be real-life {{Foreshadowing}} for how useful it would be [[note]]It's worth noting that the manga version of Summoner Monk does not require the player to discard a Spell[[/note]].
** Blue-Eyes being called outdated by Willie for having no effects became true for a quick while... and then cue Blue-Eyes getting support during the Synchro era, a Structure Deck that plays on Blue-Eyes being a Normal Monster, ''Shining Victories'' releasing even more Blue-Eyes support, and finally the promos for [[Anime/YuGiOhTheDarksideOfDimensions the 2016 movie]] giving yet more support, and the continued support onwards. Seems that Kaiba got his revenge on Willie and then some.
** Overall, several of the cards introduced in ''R!'' would go on to have a fair amount of meta-relevance, such as Beast King Barbatos being used in many anti-meta decks as an easy beatstick, Melody of Awakening Dragon being a quick Blue-Eyes search, Summoner Monk being a very popular swarm card for a good long while, and Machinas debuting in the manga. Even now, some of the cards that have yet to be released, such as ''Cosmic Space'' and ''Battlefield Tragedy'', would have quite an impact on the card game if they were [[note]]''Cosmic Space'' would auto-kill every Xyz and Link Monster out there unless it were rewritten to account for them, and ''Battlefield Tragedy'' would be seen as an easy way for an offensive player to fill up the Graveyard.[[/note]]
* OneSceneWonder: For all the hype the Evil Gods get about being dark counterparts to the Egyptian Gods, the latter barely ever appear in series, making their rare appearances this.
** Slifer gets subjected to the WorfEffect, but returns to absolutely flatten Cedar Mill in a single panel.
** Ra also gets a HopeSpot before fading away, but it's worth it for the brief OhCrap moment it gave Yako.
** Obelisk finally shows up during the final duel with Yako, [[spoiler:gets powered up to match the Wicked Avatar, and then both Gods destroy each other quite epically.]]
* TheScrappy: Honda spends most of Jonouchi's duels telling him to stop losing and doubting he can win, and in his worst moment [[spoiler: assumes Joey encouraged Reiko to attack him to score a cheap win, instead of trying to get her to actually enjoy dueling]]. Thankfully for the last act of the manga he gets RescuedFromTheScrappyHeap, having a BackToBackBadasses moment with Jonouchi and encouraging Jounouchi before his final duel with [[spoiler: Bandit Keith]].
* TearJerker:
** [[spoiler: Seeing Yami in despair, watching Anzu's soul fade away as they reach out to each other, is not easy on the heart. Gekko knows it too, and despite not knowing him for as long, the reader can sympathize with him after seeing him in a raw state of emotion after being composed for most of the series.]]
** Yakko's backstory. [[spoiler: His whole life he felt inferior to his brother due to Gekko's "perfect" playstyle, finally snapping when he lost the only parent he'd ever known.]]
** Yakko's reaction when [[spoiler: the attempt to resurrect Pegasus fails.]]
* TheyWastedAPerfectlyGoodCharacter: Bakura makes no appearance in the manga whatsoever. This is especially noteworthy as it is his dark half who killed Pegasus, leaving Yako to foolishly ask Bandit Keith about Pegasus' fate.
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