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Another new feature is a password back-up.

Both Mickey and Minnie are identical gameplay-wise, and the costumes they receive don't differ from each other in any aspect except aesthetically.

The costumes include a sweeper, which can suck enemies and turn them into coins, a safari suit that can climb walls and swing from hooks and a cowboy suit that shoots corks and maneuvers by bouncing. The latter two outfits can be upgraded at a shop.

The Genesis version of the game includes a cosmetic change for the stage 5 boss and an extra room in stage 3.

Magical Quest 2 GBA Cover

Cover art to the Game Boy Advance version titled "Magical Quest 2"

In the GBA version (retitled Disney's Magical Quest 2), Mickey's eyebrows are removed during closeups of Mickey and the character select screen is different because Mickey had a slightly short face change appearance after the game's original release. A save feature was added in the GBA Version as well.