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The underwater palettes are handled in an entirely different way on the Game Boy Advance, meaning Sonic's life icon stays the same colour at all times. Sonic himself is a noticeably different colour, and objects such as monitors and switches adopt a real underwater palette, rather than on the Mega Drive where the underwater changes are less obvious.
The changes mean that on the Mega Drive, underwater sections of Labyrinth Zone are much darker.
All of the retractable spikes in Labyrith Zone are flipped the wrong way.
There are no rotating palettes for the lifts.
Large air bubbles cannot be found in Genesis. Instead, the game uses the graphics for the medium-sized bubble to give Sonic air, and it rises differently from the ground.
Underwater doors don't use the underwater palette.
Flip the switch to reverse the lifts, and the corner wheels don't reverse direction.