A word of caution before you enter Wily's Fortress - You cannot leave the fortress between levels, nor can you save progress on how many fortress stages you've completed. Once you enter the fortress you have to do it all in one sitting. Stock up on bolts and don't enter the fortress without having stocked up on all the supplies you can buy. Make sure you have a full stock of Energy Tanks and a Mega Tank, at the very least. If you need bolts, take the Jewel Satellite to a stage with a never-ending Terry supply, stand at the production pipe, and leave your system for a few hours.
Now for the actual level. The stage starts out similar to Concrete Man's, so equip the Jewel Satellite to keep yourself safe. As you progress, you'll meet giant shield-toting robots that resemble Guts Man - use the Laser Trident to cut through their shields, and they'll fall quickly.
Propeller platforms can be found in plenty of places early in the level - use Tornado Blow to propel them upwards. Just be careful not to jump into the spikes while you've got the Tornado effect going. After using the item, recharge it to full power - you'll want it for the miniboss.
The miniboss is the fire dragon from Magma Man's stage. If you recharged the Tornado Blow, go nuts with it and obliterate the dragon. If not, Black Hole Bomb makes a fine substitute. Basically, use the same strategy as before.
You'll eventually come to a seemingly-impossible section with flame blasters. To get through here, freeze them with Concrete Shot. It may take some practice to get this section down, but once you do, it's not too tough.
The boss of the stage is a strange collection of heads with a spiked ball in front of each of them. You need to fire at the ball so it hits each face and they explode. In turn, a new head will come out. This strategy is to be repeated until they die. A few words of caution - first and foremost, never let one of the heads get its spiked ball to the side wall of the arena. If they do this, the ball resets, but they will begin firing arrow shots that are tough to dodge. Also, be warned that touching the ball is instant death since it has spikes on it. You're free to experiment with Master Weapons if you want to (Plug Ball is easy to spam if you're on the same level as one of the heads and balls), but you will probably want to opt for just using the arm cannon here.