So, the breakthrough: I figured out the final confrontation between the heroine, the minor-character-turned-secondary-heroine,
I do know it's going to have something to do with water.
ETA: I think the main problem I'm going to have is establishing why, after the two bad guys are dead, their generals are able to use common sense and do the right thing instead of doing what most people would do and grasping at the last remaining fibers of power. Say you're marching towards the site of a future battle, and all of a sudden your two top guys are dead. You don't just start taking orders from the people who killed them, which is essentially what I'm having them do at this point. Humph. This might be tricky. I'm going to have to establish at least one of them as an actual character, and a good guy at that, and then give him a reason for returning to the city instead of continuing on and killing a bunch of innocent people, other than 'it's the right thing to do'. Because it was the right thing to do when the top guys were still alive and you were prepared to do the wrong thing... why? Where the bad guys holding something over you?
Oy, now I'm rambling.