The boss battle "begins" with a short cutscene of Dr. Eggman wearing a scuba outfit deploying bombs that cause the water level to rise, initiating a short segment where the player must avoid being crushed in between the rising ground and the ceiling. After this segment, the player enters the cockpit of the Egg Mobile with the Waterspout and Depth Charge attachment, allowing them to control its movements. The player can move the Egg Mobile left and right using , and activate the impeller beneath the craft by holding any of the jump buttons.
During the subsequent phase, Eggman will be swimming back and forth in a large pool of water underneath the player. To attack Eggman, the player must use the Egg Mobile's impeller to suck up him out of the water and into the produced water plume; once Eggman hits the impeller, he will take damage. While in the water, Eggman will try to swim away, but once he is in the water plume, he will be rendered helpless until the player disables the impeller by releasing the jump button.
For defense, Eggman will deploy floating bombs that are susceptible to getting sucked up by the player too, and will damage the player if they touch the Egg Mobile. The depth charges on the Egg Mobile, which can be deployed by pressing down on , can also be used to destroy the bombs by dropping them down on them. However, the depth charges will bounce off Eggman himself.
After four hits, Eggman's scuba suit will explode and he falls off the screen in defeat. The player can then hover to the right to find the Goal Plate and finish the Act.