Final stage. You've made it at last.
If you're low on weapon energy (and you think you're going to need some for whatever reason), kill yourself and continue. You want full energy for Beat! And hopefully you've saved some Energy Tanks from the first fortress stage. You did do that "kill yourself and get nine tanks" thing, right?
This is a short, simplistic stage that doesn't even merit a walk through. Wily is waiting at the end.
Form 1: Wily Machine 5
Wily's first form in this battle is a giant skull tank. His main attacks are firing shots from the tank, which come in various varieties you need to make yourself aware of, and trying to suck you in with a vacuum-like contraption on the front of the machine. To win, fire your Mega Buster at the vacuum/cannon thing on the front of the tank.
Form 2: Wily Capsule II
Wily's second and final form is the usual "appearing and disappearing saucer." Call Beat and let him thrash Wily. With Beat on the scene, this fight is a walk in the park. Dodging Wily's shots is really all you need to worry about.
And that's all there is to it, you've beaten Mega Man 5!