Starting over won't help you. Not yet.
I'm gonna go off on a limb and say you're trying to write a high fantasy adventure in the vein of everything you love to read. Good guys, bad guys, magic and/or spaceships, epicness, etc. Amiright?
I'm also gonna guess that when you say your characters found their voices, you only mean the unlikely band of heroes. Maybe some of the villains. But that's about it. Right?
If I'm wrong on any of these guesses, good.
I'm not gonna guess here, though: your plot stinks. You said it yourself. The heroes are going to kill the bad guy but you're not entirely sure why. What's more, you're not entirely sure what's stopping them (physically and ethically) from just marching straight in and lopping his head off.
The big question, really, is why?
Why does the bad guy need to die and why does the hero need to kill him? Why doesn't anyone else get involved? Why do the bad guy's henchmen follow him? Why doesn't the hero just hop a plane to the bad guy's hometown and lop his head off? Not just in the sense of physical obstacles, but ethically why?
If you want a good hero vs villain story, learn from the comic books and develop your villains. Think about it. How many stories do you remember from comics, especially if you haven't read in years? Which ones do you remember?
I remember X-Men vs Magneto. I remember Batman vs Joker. I remember Spidey vs Green Goblin. I don't remember anything about Spidey vs Vulture other than that the Vulture a) can fly and b) is old. What makes a good villain memorable? It's not their powers or their characteristics or any of that. It's that they define and are defined by the hero. They share some kind of connection. How is your villain connected to your hero? Why can't it be anyone else to defeat him?
Develop your villain, look at the story from his point of view, and the plot will start to take care of itself.
If things ever get too linear, throw rocks at the hero. Or the villain. There should be at least four major conflicts or twists preventing the hero from reaching his goal. They should all be different. Maybe a fight breaks loose one time. Maybe the bridge gives way the next. Maybe they get poisoned in a blizzard. Mix things up, and always undermine your expectations.
Go nuts.
Then rewrite it.