Walkthrough: Siege on Nino Island, Part II

Glyde's Birdbots aren't even close to being done with Nino. Looks like MegaMan's still on the job...

Deal with Data, then go to the next door with the light above it. You have a boss of sorts here, the Birdbot Carrier. Start off by blasting the two Birdbots in front of you, then head left along the dock and take out the ones running towards you. Use your Buster (not Cannon) to shoot the carrier at its current position. However, make it a priority to defeat any Birdbots that come out.
When the ship starts to move, head to the opposite side of the docks and lock onto it. Now is the time to start unloading as many Buster Cannon shots as possible. When the carrier arrives at Johnny's ship (that's the red one), it'll start releasing Birdbots again.
Don't let any Birdbots get past you, as they can start blasting the door down and you'd never know. However, wait for them to get on solid ground first--sometimes they manage to fall into the ocean without you ever touching them.
Keep belting the ship with Buster Cannon shots, and the battle will be over in no time.
Back inside, do your business with Data, then take the elevator up. Equip the Lifter, and climb the ladder.
The big yellow panel in the middle of the roof is the Birdbots' target this time, so watch out. Ignore the flying ships, and watch for Birdbots that drop onto the rafter.
You'll have to divide your attention for now. There are four rafters, each one connecting to a side of the platform. Lock onto the Birdbots and blast them off!
If they get too close, they'll throw a bomb onto the platform. You can use your Lifter to pick those bombs up. When you do so, throw them back! Keep blasting the Birdbots.
Soon, the Birdbot Command Carrier will fly up. Boss time!
You don't have to worry about guarding the hatch any more. For the most part, the ship will just fly around in circles and shoot bullets at you. Lock onto it and let fly with Buster Cannon shots. It should be pretty easy.
However, it does have one noteworthy attack--ramming you. The easiest way to dodge this is to just roll out of the way.
Soon, you'll do enough damage to make Glyde's forces retreat for the time being. Looks like they're heading back to base...
Go back to Ruminoa City and the Digger's Guild, and talk to Johnny and the guildmaster. He's not done with you yet--it seems he wants MegaMan to go to Calbania Island and destroy Glyde's base.
Back aboard the Flutter (it's fully operational now), give Roll the Cushion you bought earlier, and also the Stuffed Doll and Model Ship if you haven't already. Then, leave the ship and come back to the bridge. Roll will be gone, and Data will tell you she went to clean up.
Go to the bathroom (the door on the left in the living room). It seems MegaMan walked in on Roll...good job, little guy. :-)
This all isn't for kicks and giggles...When you go back to the development room, Roll will tell you she bought a tool kit that gives you a ten percent discount on all upgrades! Sweet!
Fly the Flutter over to the deserted Calbania Island in the southeast.

Go:
Backward: Siege on Nino Island, Part I
To the Walkthrough Home
Forward: Calbania Island