In the Wii version of the game, the player must swim to a giant glass dome with a lever inside. You will be followed by homing torpedoes, so use one of them to break open the dome. Also, sometimes the homing torpedoes (the white ones, by the way), have a drill wisp inside them, which will be useful for the fight with Admiral Jelly. Flip the switch with a Homing Attack, or by jumping onto it to flip it, and the fight will begin! Admiral Jelly arrives with a bunch of pirates, and when he spins to the side, use that time to destroy the pirates. You can only hurt the Admiral when he is standing still, so be ready. Do this a maximum of 3 times to destroy him. If you managed to get the Drill wisp, from the torpedoes on the ship, you can use it to cause double damage, with the only catch being that once you activate the drill wisp, Jelly will bolt off in a random direction at full speed, thus making it harder to hit him in drill mode, and a red eggman arrows will point towards his direction, making it easier to find him. BUT, if you are in chase mode with A.Jelly, he may change directions suddenly, so it is recommended that you learn to use the drill boost at the correct times, in order not to waste it up all at one time. And also remember that Wisps deal double damage, and thus making it possible to kill him in two hits. And it takes three hits without the drill wisp to kill him normally.
The Admiral has the same appearance in the DS. This time, he will only use two pirate minions to attack. Depending which side Sonic is on the platform, Jelly will turn his para-scope into a cannon and launch a minion onto the platform. Sonic must stomp the other side to hit Jelly with his minion. Jelly will fall, and Sonic must hit his head to deal some damage. If Sonic boosts into his head, he will gain the Cyan Laser power to deal double damage. Jelly's attacks will get stronger, making it harder to hurt him in the 2nd phase. Keep hitting him until his health is at 0, then hit his head once more to kill him.
In both versions, Sonic must collect air bubbles to restore his breath.