If the people in your story are at war, there are a few things you might want to ask yourself. For starters, why are they at war? Does anyone remember, or has it been so long that no one remembers or cares why they're fighting, they just keep fighting? Is the hatred based on an actual slight by one of the people, or just a simple disagreement? Or is it just because they don't like the way the other looks?
Knowing this helps define both the story line and your character's motivations. Your villain could be out to continue the war just to continue the war, or because he's looking for something that the war would reveal. Your hero/heroine could be seeking to end the war, one way or another, or to keep that "something" out of the villain's hands.
Your hero/heroine could have conflict about accepting help from the other side, even though he/she might need the help, or be captured by the other side and then have to find a way to freedom before he/she can finish his journey.
Maybe he/she finds out the war is nothing more than an argument over the price of cheese, and manages to find a compromise that not only ends the war, but stops the villain. Or maybe the bigger problem was an assassination that one side was blamed for, but, in reality, had nothing to do with it. Speaking of which, I need to finish that story. XD