In the Wii version of the game, the player must swim to a giant glass dome with a lever inside while being followed by homing torpedoes, which must be used to break open the dome. This boss battle is similar to the Sweet Mountain boss battle, but unlike the Sweet Mountain boss battle, it is more difficult. When the switch is activated, the player then faces Admiral Jelly. Admiral Jelly arrives with a bunch of pirates, and when he spins to the side, the player can use that time to destroy the pirates, and hit the Admiral when he is standing still. Admiral Jelly requires a maximum of three hits to destroy him.
Some of the white homing torpedoes have a Yellow Wisp inside them, which can be used to deal double damage. The only difference is that once the wisp is activated, Jelly will bolt off in a random direction at full speed, making it harder to hit him in drill mode; a red arrow will point towards his direction, making it easier to find him. While the player is chasing Admiral Jelly, he may change directions suddenly, so it is recommended that the player learn to use the drill boost at the correct times in order not to waste it.
The Admiral has the same appearance in the DS version of Sonic Colors. This time, he only uses 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 damage. If Sonic boosts into his head, he will gain the Cyan LaserColor Power to deal double damage. Jelly's attacks will get stronger, making it harder to hurt him in the second phase. The player must hit him until his health is at zero, then hit his head once more to kill him.
In both versions, Sonic must collect air bubbles to restore his breath.