Walkthrough: Glyde's Base

With Appo and Dah's help, MegaMan has made it into the fortress. His goal is to completely destroy it, but that means getting Shu out of it first. You'll have to make your way through several defense units before you find her and the detonation switch.

You'll be at an airport for Glyde's ships. The goal of this area is to take out all the enemies, and then you'll get a key to the next section of the base.
First, take out the ships that are still on the ground.
Then, go for the airships with the Buster Cannon. Since Data is right outside the base, feel free to unload all your ammo. Shouldn't be too hard.
The turrets on the wall may be a nuisance, but you aren't required to destroy them to move on.
Once all your adversaries have gone boom, you'll find Door Card Key 1 floating in the center of the room.
You can go out the north door to find Data. I recommend coming back to him every time you finish one of the base's areas to recharge and save.
Back inside the base, go through the west door into the next area. The goal of this particular area is to take out the Birdbots sniping you from the top of the tall tower.
First things first; take out the cannons posted on the wall.
The Birdbots will throw bombs down at you, but they're easily avoided, so long as you don't forget to notice one landing next to you. Target the Birdbots from below and shoot at them with the Buster Cannon. Keep doing so until they're all gone.
Eventually, the tower will explode and you'll get Door Card Key 2.
Search the fridge in the area where the tower was to find a Fried Chicken, a recovery item that will restore all your health. If you can, don't use it unless you're absolutely going to die. You'll need it in the game's final stages.
Also, search the cabinets where the tower was to find the Accessory Pack, a great Buster Part. Equip it and the Power Raiser, then go back to Data, then go through the south door in the tower area.
You'll be in an area with three Glyde Tanks. Just target them, and circle and shoot. Try not to lose sight of one of them. You'll probably get shot a lot, unfortunately. Whenever you're not being fired at, unload a Buster Cannon shot. When they're all gone, you'll get Door Card Key 3. Go back to Data before continuing east.
You'll be in the barracks. Birdbot Tanks are rolling around, so hide behind buildings and take them out with Buster Cannon shots as they roll by. They're not hard as long as you stay out of their path. When all three are gone, feel free to blow up the buildings.
Use your Lifter to pick up the crates scattered around the area, then throw them under the balcony, where the blue panel is. You'll have to stack at least two crates to be able to reach it.
Once two of the crates are stacked, MegaMan will have just enough height to grab onto the railing and pull himself up onto the balcony. Go through the door.
You'll find a storage chamber, where a few Birdbots are guarding Shu. They shouldn't be hard to take out at all. However, one of the Birdbots will activate the self-destruct mechanism!
Now you have less than a few minutes to get out of the base. To make matters worse, the exit is guarded by Glyde Tanks, and the Birdbot Command Carrier you fought on Nino Island will be attacking you at the same time. Ignore it and Shu for the moment, and take out the tanks blocking the door.
Once you've done that, go find Shu and use your Lifter to pick her up. Head for the hills!
The two of you will escape just in time as the base explodes behind you. When you get back to the village, Shu will give you a Cute Piggy as a reward (uh...thanks?). Now, you can choose to explore the optional Kito Caverns on this island, or you can continue back to Nino Island for a final round with Glyde's forces.

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Backward:Calbania Island
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Forward: Kito Caverns (OPTIONAL)
Forward: Siege on Nino Island, Part III