This is the end of your book, right? The
most important thing is that your ending can't be
cheap.
I'm going to get on a soapbox, I've seen enough bad endings that I don't want to see another. This is me as a
critic. First, let's lay some ground rules:
1. No silver bullets.
2. No dirigibles.
3. No cavalry.
4. No miracles.
On silver bullets -
It's perfectly okay to give the villain a weakness. Werewolfes with silver bullets, Evil Overlords with strange magical artifacts, vampires with just about anything in the book. It's almost a standard in fantasy. But it's cheap as hell.
If you use a silver bullet, it MUST fail at the crucial moment. Make the gun jam, make the artifact run out of mojo juice, make the kryptonite turn out to be a dud, make a stormcloud block the sun moments before the hero opens the window to let the sunlight fry the vampire.
On dirigibles -
Once upon a time, a story ended with a dirigible crashing and killing everybody. Don't make your villain spontaneously burst into flames because the hero can't feasibly win. The villain might as well defeat himself, because the hero's victory is going to be completely hollow.
On the cavalry arriving at the nick of time -
There's a word for people who show up at the nick of time and save the day. That word is "hero." If your hero gets bailed out by someone else, then who's the real hero of the story?
On miracles -
See dirigibles, above. No having your hero's mutant powers awaken during the fight.
Now, feel free to ignore the rules. Maybe your story's meant to be a sort of eye-opening thing where the villain wins or the hero has to cheat to win (and thus you show that he's not so heroic afterall). There's only one question you have to ask yourself when you consider how it ends and how the hero's going to win:
What are you trying to prove?
Simply put, if one of your themes is, say, virtue vs hubris, then figure out a way to make the villain's pride be his downfall, or the hero's virtues be his. If what your story is trying to convey is that a dangerous villain needs to be put down at any cost, then maybe you could have your hero cheat (bring a gun to a fistfight, use poison on his blades, etc). Maybe your hero sacrifices himself to hold the villain in the facility while his allies blow it up, ensuring that both die?
I'm assuming that your hero's heroic and your villain's villainous, so you want this to be a fair fight (at least, the hero's not going to cheat) and you want a clear win. I'm going to take two quotes from
The Lester Dent Pulp Paper Master Fiction Plot:
The hero extricates himself using HIS OWN SKILL, training or brawn.
...
Did God kill the villain? Or the hero?
Skill can be anything. Intelligence, a special ability, or maybe even perseverence of a virtue. Depends on what you and the hero are trying to prove by that fight.
So, let's see... I don't know much about your hero's skills, but you've told me this about your villain: he's got combat training, he's got speed, and he's got a weak point.
If you're looking for a good, solid ending, the weak point shouldn't spell "insta-win." Maybe a distraction, but if the villain's worth his salt, wouldn't he have planned specifically
for the instance of somebody attacking his weak point? If
I were him, I'd have had the nerve endings deadened (at least for pain) or maybe even re-arranged. It's a huge liability, especially for anyone who has any combat experience.
Apart from the above, there are pretty much three ways your hero can win in spite of the clear advantages your villain has:
1.
Remove the advantage. Maybe the hero floods the room with molasses so the villain can't move as fast?
2.
Adapt to the advantage. Maybe the uses the
Space Invaders strategy and, instead of trying to hit the villain head-on, attacks where the villain is
going to be? Maybe the villain falls into a pattern that the hero can exploit, or maybe the hero sets a trap.
3.
Take advantage of the advantage. I fenced in college, and everyone once in a while I'd come across some guy who fought real aggressively,
jumping in and attacking as fast as possible. I would reverse-lunge/duck (ie, move out of the way) and stick my sword out so the tip was where he was about to land. The moral of the story: the faster they are, the faster they impale themselves. Your villain might not be that stupid, but
any trump can be turned.
Just keep at it, you'll figure something out.