Much like the previous stage, this one is simply an "item room" followed by a fight with Mega Man's arch-nemesis. Grab the items and move forward. You will need Hard Knuckle, Top Spin and Rush Jet.
Like the previous Wily fight, this one is broken into two parts. The huge "peace-keeping" robot occupies the entire screen. The blue head of the machine will fire shots at you in the same pattern as New Shotman. Simply dodge these shots, and fire Hard Knuckles at its ugly mug. After about four hits, the face will explode....
Gamma & Dr. Wily
....And a new cockpit will lower, with Dr. Wily at the helm! The two things you need to look out for here are the giant hand that comes at you from the bottom right corner of the screen (although the flat top of the hand is safe and can be used as a platform to reach the ledge), and of course, the fired shots from the robot itself. There are two ways to win this fight: you can use either Top Spin or Search Snakes. The former is much quicker and will end the fight a lot faster. Simply activate the spin and dive at Wily's cockpit dome. Dead. Simple as that. For Search Snakes, use the platform and aim at Wily himself. This is a little more tedious and time-consuming than the Top Spin method, but if you want an added challenge, why not give it a try?
And that's all there is to it, you've beaten Mega Man 3! Kick back and enjoy the classic ending!