This is amazing. If Yuffie's dialogue had actually been anywhere near this good, in KH or FF 7, they would have been much better games. And it's not just Yuffie. You've gone past "in character" to the way the characters should have been.
The tone, too, is phenomenal. The end of the world feeling, with everyone vanishing, everyone dying, Cloud going crazy, on and on. Your Yuffie's so spastic - usually that's hilarious and then all of a sudden she does something that's so lame it's beautiful, like kissing the microphone. You have a gift. Thank you for writing this.
But fix your formatting, please. I don't know if it's the site or what, but your italics are all screwed up in every chapter. It's distracting from the awesome story.