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Question
Say someone writes a fic wherein it's sort of a fusion between Fandom A and Fandom B, but no characters from Fandom B are actually in the fic itself (basically, characters from Fandom A coexist in the same universe as Fandom B), does this get labeled as a crossover?
I think AO3 has a "fusion" option, but I also don't want to post something that shows up in searches for both fandoms and have someone click it hoping for characters from Fandom B where they simply are not there.
I think AO3 has a "fusion" option, but I also don't want to post something that shows up in searches for both fandoms and have someone click it hoping for characters from Fandom B where they simply are not there.

no subject
I personally don't consider it a true fusion unless characters from Fandom A are transplanted into roles originally inhabited by Fandom B's characters, but I suspect this is a slightly antiquated view by now. I'd say you're fine tagging it as either a fusion or crossover (though others may disagree on the latter).
The thing I would strongly suggest is: don't tag Fandom B as a fandom, especially if Fandom A is a big one and Fandom B a small one. Between my own experience as a mostly-small-fandoms fan and discussions I've seen around the place, I can say that this is a surefire way to raise Fandom B fans' ire. XD; Declare the fandom you're crossing Fandom A over into in the additional tags and/or summary instead, and then it will still be searchable for anyone specifically looking for a crossover like that.
no subject
I've come across more than a single "crossover" where no such thing exists, and completely understand how frustrating that can be.