Had the same problem here, well you got 3 choices,

1. Start the game all over (and sacrifice all your hours >.<)
2. Kill the Bastard when your strong enough (the most painfull choice)
3. Kill Dark Bahamut with Yojimbo's Zanmato which slices him in little pieces :joey:

I made choice one (I was at 78 Hours) but that was cuz i missed the treasures in some temples so I couldnt get Anima and Magus Sisters ;/.