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These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Yu-Gi-Oh! The Thousand Year Door
Beam Me Up, Scotty!: The Queen's true form is never referred to as "Demon Chaos Queen" in the text of the story, only referred to as that in the notes where the card is put into OCG terms. The author has stated that this may not have truly even been a card in the physical sense, at least as far as her deck was concerned, but simply the Queen herself becoming part of the Shadow Duel.
Cry for the Devil: In Redux, Stan, Francesca and Andy find out from Rudwilla why she became the Shadow Queen. Later when the Shadow Queen tells them how, Andy tries to reason with her only for him to be brushed off by the Queen when she admits that she doesn't regret her decision.
Andy: And decided not to stop there, I take it, Iris, it wasn't their fault for what happened to your brothers…
Iris: Oh, spare me! Like I've never heard that before, the old 'it didn't have to happen the way it did' routine. Let me tell you something, Andy… Maybe it could have turned out differently… But I like how I am. I never regretted the deal I made with Graz'zt for one minute, not even during the eight months of horrid pain I spent at that facility. I actually liked the pain after about a week, and the pain made me feel power, which I liked even more… I still like it! Love it, in fact.
Missing Chapter: In the original fic, there is a chapter in which Stan duels Johnson of the Big 5 from the original Yu-gi-oh series which was only posted in a site called Pokemaster Forums, but is completely absent from the chapters posted on fanfiction.net.
Moral Event Horizon: The author has stated that the Queen's murder of Count Bleck was supposed to symbolize the point where she crossed this line, at least in the present day. (Andy's angry reaction to it was supposed to express it as such.)
Old Shame: Cyber Commander has regretted his "extra" Dark Scorpion cards, since they completely miss the theme of the Dark Scorpions (Five-Man Band), and the character of Wanda Underwood, as she's blatantly a repetitive, spiteful bashing of Weevil Underwood. He's since banned any other authors from using his Dark Scorpions and never used them again, and Wanda doesn't appear at all in Redux, her duels replaced with new characters.