You can certainly have a cross over between video games and anime, since often they do have a symbiotic relationship, as you say. But we are going to need at least one fandom listed in the initial disclaimer, with a note that additional fandoms will be disclaimed in the chapters in which they occur.
So, for example, let's say you use Devil May Cry as the "main" fandom. That lives in the Games subdomain, so that's where you post the story. The initial disclaimer looks like this: "I do not own Devil May Cry and the other fandoms listed in each chapter, and I make no money from this story." Then, since Hatake Kakashi shows up in chapter 1, at the top, you add an additional disclaimer: "I do not own Naruto and I make no money from this story." Those additional disclaimers don't count as Author's notes, and you can easily add multiple fandoms there: "I do not own Naruto, Bleach, or Death Note and I make no money from this story."