I have no words. I'd heard the ending was something else, and it did not disappoint.
I fixed the error by leaving "Keep Instruct" and "Dialogue Single Player" off in the System menu. I don't think I have the save anymore though.
I'm getting an error "cannot read property 'addstate' of null" when the second battle starts.
EDIT: Apparently I'm getting the error because I turned on "Keep Instruct" and "Dialogue Single Player" in the System menu.
