Mickey and Minnie Mouse travel by bus to the circus at the edge of town where they are going to spend the day. When the bus arrives, a little late, Goofy appears and tells Mickey and Minnie that everyone in the circus tents has disappeared. Mickey and Minnie are surprised by Goofy's claim, but choose to go to the circus and see it with their own eyes. At the circus they realize that their friends Pluto and Donald Duck are gone. Mickey and Minnie must now find out what is going on at the circus.
The game ditches the alternating two-player method in favor of simultaneous co-op. 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.
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.