This idea is one I've seen done before on a couple of occasions, but I'm not sure I've ever actually seen it go past the sports festival in terms of the plot. I know the idea could be possibly seen as overdone, but that's more so due to the amount of chapters they usually have than how many actually do the idea.
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In this idea, I pretty much want the setting of Classroom of the Elite to have multiple genius characters from other series included, and for the plot to change depending on certain decisions by the characters. You are free to add whatever series' characters you want to this list. Some recommendations I have are Light and L from Death Note, Lelouch from Code Geass, Sora and Shiro from No Game No Life, and the main girl from Kakeguri included. (I don't know her name; I don't even know if I've spelled the name of the series correctly, but for reference it's that gambling anime.) There was also a character named Victoria, or something along those lines. She would be interesting to see involved, but I don't even know the anime, so I can't really be of help there.
Rather than the characters facing each other with them being spread out across different classes, I more so like the idea of them all being in one class, titled something like "classroom 1-E". (This works particularly well because you can say that the "E" stands for "experimental".)
(Some of the writing below assumes that you've included the characters I mentioned in my recommendations, so ignore those pieces of text if you don't wish to encompass them within your story.)
I want L to be investigating both Light and Ayanokouji, and I also want each of the characters' respective powers in each series to hold true in this fan fiction. In other words, I want Kira to exist and still be killing people with the Death Note in the world of Classroom of the Elite, and I also want things like the geass from Code Geass to exist.
I want Ayanokouji to gain his own supernatural ability at some point in time; it can be a power or ability from a series already included, or it could be an ability from an otherwise completely unrelated series. You could even come up with an entirely unique power that isn't from another series. This is all so that he can resist things like the Death Note or geass if they are used on him, so maybe even just give him the ability to resist the supernatural. If all of that is too complicated for you to manage, you can loosely allude to certain abilities existing without actually involving them in the plot.
Not every character in this crossover has to be a genius; I just want the ones that are geniuses to be in a special class with Ayanokouji. In other words, you can have non-genius characters included, but they must not be in the class of geniuses if that is the case. So as to not disrupt the plot any further than necessary, I'd also prefer if you put them in the second or third school year rather than the first.
Don't have it so that Ayanokouji goes unnoticed by the others in his class; they are geniuses as well, so it's only natural that they'd notice if he held back. Plus, it's a class for geniuses anyway; they wouldn't really be geniuses if they didn't notice that detail. I want Ayanokouji to give up on having a peaceful life early on in the story, right after he realizes what that his class is experimental and full of geniuses. He should still unconsciously hold back, however, and the others should continuously have to remind him to not do so, at least early on in the story.
Sora and Shiro are allowed to play chess with anyone, but if they play against Ayanokouji it must be a stalemate, so that neither of them truly lose. If you don't like this, you don't have to adhere by it, but I'd still prefer if you did.
Everyone should be easy opponents for the class, and I don't want that whole "judged more harshly for behavior because there're less students" thing to exist. I want them to demolish everyone in the special exams, basically, unless there is a good reason for them to not do so.
If you ever get this fan fiction to the part of the story in Classroom of the Elite canon where the white room enforcers start coming and Tsukishiro exists, then have the whole class start being suspicious of Ayanokouji, and have L gain information on him more easily.
It should not be solely Ayanokouji's perspective, though I'd prefer it if when it is his perspective you make it so that it's his true thoughts, and not that facade he puts up in his thoughts at the beginning of the series. Have L's perspective shown frequently after significant reveals or events, as I'm interested to see his thoughts on things that happen.
Have it so that they all focus a lot on recordings events, so that they can use information for blackmailing. Honestly, after reading the various fan fictions focusing on it, I'm kind of disappointed that they haven't been used this way in canon so far. Have this happen especially during the beginning of the story, with events like the meeting between Suzune and Manabu, or the reveal of Kushida's nature.
Have Sakayanagi and Ayanokouji's conversation in the sports festival be witnessed by someone from his class; I'd prefer it to be L, but you could make it anyone, really.
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A rather long first chapter, but hopefully it got across just how much I like seeing these kind of fan fictions, and hopefully someone picks this up. You're free to change up whatever you'd like; you don't even have to use the central ideas I put down necessarily, I just want something similar to this to be updating again. Thank you for reading all of these paragraphs of text.