Mega Man/Wily Fortress 3

After defeating the clone, Mega Man is able to gain access to the sewers beneath Dr. WIly's fortress and use them to get closer to the control room in the heart of the fortress. Dr. Wily didn't think anyone would actually try to break in this way, so he only set up a minimal defense against intruders. This makes the third stage the simplest out of the four Dr. Wily stages. Once you reach the pipe at the bottom, it's literally a straight shot to the boss.

Stage

 * A: You start at the sewer entrance, you must make your way down to the pipe at the bottom. Along the way, you will only encounter two types of enemies: Suzys and Screw Drivers.  While some of the Suzys are vulnerable to attack, many of them are positioned in drops and are difficult to attack directly.  If you recall, the Rolling Cutter will not only eliminate them in one hit, it's always quite useful for hitting the Suzys that are slightly below you, so you can use it to make the way safer.  As for the Screw Drivers, the ones you encounter are mounted on the ceiling.  Unless you feel like using the Thunder Beam to attack them from below, wait for them to fire and simply run beneath them when they stop.

(Alternate strategy) Run at full pace and maintain a jump tempo to jump over all the enemies
 * B: Once you reach the pipe and run a short distance to the right, water will suddenly rush in and flood the pipe. The current of the water will be so strong that you will be pushed along to the right if you stand still.  You will be prevented from trying to run left, and will move entirely too fast if you run to the right.  It's recommended that you sit back and let the current take you where it will.  Along the way, Pepes will fly in from the right side of the screen.  If you stand still and fire at a constant pace to the right, you will take out each one as they appear.
 * C: Further along in the pipe, the Pepes will stop appearing and you will enjoy a brief peaceful moment. That moment will be interrupted by the appearance of Killer Bombs.  In theory, they are no different than fighting the Pepes, except for the fact that they explode when destroyed.  This makes it all the more important that you shoot them down as they appear, before they have a chance to get too close to you.  If you keep up the rhythmic shooting to the right, you should have nothing to fear until you reach the end of the pipe.
 * D: You will eventually arrive at the end of the pipe. Killer Bombs will continue to appear, and the current will continue to push you ever close to the door.  Whether you're ready or not, you'll have no choice but to head inside and fight the boss.

Boss: CWU-01P
The boss stationed at the end of the sewers is a bit unusual and unlike any other boss in the game. Rather than fighting against one machine, you must fight against a set of machines; seven to be exact. The CWU-01P is a machine designed by Dr. Wily to patrol and clean the sewers. They are able to envelope themselves inside a bubble to keep their circuitry dry. All seven operate at different speeds, and they enter the room in order from the slowest to the fastest. They enter the room through one of the three chutes and proceed to roam around the edges, firing bullets at intruders. Each machine that appears moves more quickly around the room than the last.

Because there are seven machines, each one is fairly easily defeated by only a few shots from your Mega Buster. However, by the time the fourth or fifth machine appears, they will be moving so fast that it will be difficult to attack them effectively, and especially difficult to avoid getting struck by them. If you experiment with your weapons, you'll find that few give you any particular advantage. They are quite vulnerable to Hyper Bombs, but they way they move around makes them difficult to hit. You will obviously notice the blocks in the room, and they are not there simply for decoration.

It turns out that using the Super Arm to pick up and throw the blocks at the machines is the fastest way to defeat them. But there's only four blocks, and seven machines. It would be unwise to pick up the blocks and toss them at the first and slowest four machines. That would leave you defenseless against the fastest machines. Instead, use your Hyper Bomb (or the Mega Buster) to defeat the slower machines and finish the faster ones off with the Super Arm. At a minimum, you should destroy the first three with the Mega Buster, but if you have a lot of health left, you should try to shoot the fourth. That will leave you with one extra block to play with in case you make a mistake and miss one of your throws. That being said, don't get too anxious when throwing the blocks; they won't come back if you die and return to the room.