You first get a tutorial on how to use your new powers with the Calibrus. Basically, whenever you see the Calibrus change colors after the first cut, you can time the next cut to make Kutaro go faster and further than with a normal cut. You'll automatically get the SUBMARINE HEAD during the tutorial. Use that knowledge to practice it after going into the gateway, where you will need to cut all of the purple webbing to continue the stage.
On the next screen, use the Submarine Head's action to get transported to the bonus stage. The next screen is where you need your new powers with the Calibrus, as there's more sticky purple webbing, as well as little pillars of fire that shoot from the ground. You can't land where the fire comes from, as it's too hot, meaning you'll have to quickly make your way across without touching the ground.
In addition to the fire, a giant saw blade will appear and chase you on the next screen. When you get to the engine, cut the smoke in the order shown to finally make your way out of the Generals' Moby sub. Captain Gaff talks about how the island is nigh impenetrable, except for one way, which involves blasting you out of his big cannon.
You should see some crabs on the wall to the left of your starting point. Keep hitting them with Pikarina until you get the CRAB HEAD. Watch out for the spiked barrels coming out of the wall, which are actually being thrown by Grubs (hit the wall to the left of the first barrel to uncover them). Use bombs to make platforms appear, which alternate between a safe spot and one covered in spikes, then head inside the "secret pirate base."
It's pitch dark in here, so go to the right until you can toss a bomb at the switch. Use the hook that appears to raise the platforms, but watch out for the electricified sparks. Outside again, you can use the Octopus Head's action to cover some gaps and allow you to spring up to some Moonsparkles. There will be more spiked barrels, but you can stop them like before.
Use the hook to make the cannon make some smoke appear, allowing you to get to the second base. Make the light turn on like before, then toss a bomb into the opening when it's on your side, allowing you to go up. Yet another electric trap appears, this one a rotating one with openings that allow you to go through.
There will be a rolling barrel being constantly thrown, along with a ramp that gives them some bounce, so be careful. Note the Blowfish Head icon here, which will make one appear and actually stop the barrels from spawning anymore. Keep going now until you reach the third base, which will start the boss fight with the two Generals.
BOSS: General Pig and General Sheep
The first part of this fight has you against Robocrab and if you use the Crab Head's action here, a real one will show up and completely obliterate the boss' legs, leading you to the second part. However, if you don't have it, you'll have to put through with the actual fight. It will move around with one leg and then stab the ground with one of its claws.
Your goal here is to grab the hook on the right leg and keep pulling to expose a weak spot. Cut this until the leg falls off, then do the same with the left leg. This will expose some wires that you can cut and make the boss abandon its legs, entering flight mode and the second stage. At first, the boss will approach from the right side and you should see a bunch of smoke; either use this to get above and not get hit, or use one of the holes in the ground (crouch).
After doing this, it will use a tractor beam to try and suck Kutaro up, but the idea is to stay out of it and toss bombs into it. Two bombs will initiate the next part, where you need to use the smoke to reach the Generals while avoiding debris. When you reach them, attack them to split them apart and then do the same on the exposed wires.
This will have the Robocrab split in half on the ground, but before you finish them off, hit both General Sheep and General Pig with Pikarina to get the SHEEP HEAD and PIG HEAD, respectively. Once you grab them, hit the Square button to initiate the QTE to end the battle for good.
