The Crystal is referred to as the origin of all existence. The center of life. I saw it as more of a subliminal symbol to long time fans. The Origin of Final Fantasy. It makes sense seeing as how the whole game is one big homage to other FFs. Why not have the history of the series at stake? Look past the exterior of the story. FF began with the Crystal(s) so if it's at stake then it's really the existence of FF at stake rather than just the World of IX. I think it was Square's way of a thank you to long time fans. Or have I completely gone overboard with this theory?