It occurred to me very recently that with the L5R game wrapping up, I'm going to be running the fight with the big bad soon. This struck me as weird because for 8 years this thing has been working in the background but never in a way that would bring them face to face with the PCs. They've been a concept, an unseen force, a lingering doom, an ever present threat....but they haven't had stats, because I didn't need them. Now I need stats, because odds are the game will come down to a fight - it is an L5R epic with a lot of bushi PCs after all - and for the PCs to have a chance at victory it has to have stats. But first, I need to consider some other things, and the questions I have to answer may help you as well.
What Kind Of Fight Is It Going To Be?
The first question I need to ask myself is what type of fight is it going to be. There are a few obvious answers to this. Some fights happen on the move - PCs and NPCs shooting at each other from vehicles as, while other fights happen in close - your more traditional in your face fight. Some fights are straight up - again, more traditional beat downs - and others are more tricky - there is a puzzle involved in the combat that has to be solved.
Knowing what kind of fight I'm want to have will also inform me on how I do the stats. For example, if the fight is going to involve environmental threats to the PCs, then the bad guy doesn't need to be, and shouldn't be, as strong unless the bad guy too can suffer these consequences. More traditionally, if the boss is going to have all her henchmen around her during the fight with the PCs, she also doesn't need to be as strong because there are other combatants around to help her.
Where Will The Fight Take Place
The fight with the big bad should always be somewhere memorable. If she doesn't have a great lair, then how will the PCs respect her after all? More to the point, the fight with the big bad is your final set piece with your PCs and often signals the end of the game. It should be memorable, and a good setting starts that off.
Consider the differences between a fight in a volcano, a castle throne room, and between speeding skyships. Each has their own flair, but some are more straight up than others and that's fine. Beyond the simple description, what else can you do to make the setting memorable? What does the villain keep around them? What will they have on them when the PCs finally confront them?
How Can The Fight Offer Unique Challenges
This one is more optional, but if anyone is going to have the ability to bend rules for abilities or have things otherwise not allowed it should be the final boss, no? This can be as simple as a means of healing from the environment the PCs have to find a way to stop (making it a mini puzzle), or a barrier that makes the villain invulnerable that has to turn off (a bigger puzzle.) Or it could be something built into the encounter itself.
Perhaps instead of countering spells, the evil wizard has the ability to reflect them back. Perhaps they can make temporary clones of the PCs. Let your mind run whild with it, but if you can bring something new it can help make things more memorable.
Dynamic & Fun
Most importantly, you want to consider how to make the fight dynamic and fun.
By dynamic I mean ways to keep the combat moving, to keep things moving around the table, and - if you can - to move people around the battlefield. Ever notice how special effects in movies have gotten better that fights have become faster, more agile, and more frantic? It's because those give a thrill and add that cinematic flair to things. You can do it in your own game too, but it does take some preparation. I personally love throwing PCs around. It's especially good as it gives a way to display power without dumping a ton of damage on people while still making things challenging.
Fun is harder, but all the more essential. Everyone misteps, but you know what sucks? Feeling powerless to do anything while the group slowly gets whittled down. Your better with a fast death than a slow, prolonged one. Ideally though, you're best off with a fight that is challenging, that pushes people to the edge, but never makes them feel like there is nothing they can do.
By the time your PCs are at this stage you should have a general idea of what they can and can't do. So use that. Build for it. Give them a fight they can win, but make them earn it. And if things are going bad, try to make it so it doesn't feel oppressive.