I also vote for Kingdom Hearts because someone once tried to explain the overall plot to me, and it genuinely sounded like he was on acid. Elder Scrolls (especially Morrowind) also has some crazy shit, especially with stuff that Michael Kirkbride adds to the story later on (he was also a writer on Morrowind). E.g., stuff like Vivec knowing that the Nerevarine (the player) can save and load his game (or at least is aware that the Nerevarine is able to tap into the meta structure of "reality"), which obviously makes any confrontation pointless on multiple levels. But I think the Elder Scrolls community has shifted to rejecting this stuff because Bethesda chose to not dive deeper into these concepts, which is a shame, imho.