This, once again, is based heavily off my experience playing the game. The final battle happens in two phases, the first phase having Mamiya's "main" theme as it's background, then a second phase, with it's own theme. The first section starts off with the full version of Mamiya's theme, then goes into the 'Final Battle" theme.
I ended it with full pipe organs to give it a bit of a 'release' at the end, breaking the tension put forth by the rapid strings in the background.
Both songs play when you confront Mme. Mamiya at the end of the game.