Hmmm, What if The "Twelve" is really some sort of Magic/Technology combine that the Allagans used to "capture" Bahamut in the past, so that they could potentially use him as a weapon. We see that the "prayers" activated what looked like "Magic" (maybe even some ancient technology) that called out the "twelve imprisonment keys" we see again go at Bahamut with a new Dalamud moon to trap him again. Could it be that Bahamut is simply pissed that he has been imprisoned and is now going to seek revenge?