One day while Mickey Mouse and his pals are playing ball in the park, Pluto falls off a cliff and into a world of mystery and magic. Following Pluto's tracks, Mickey must walk, run, hover, duck, and jump through six levels of giant vines, strange creatures, dangerous mountains, raging fires, and other magic-enhanced hazards in order to rescue Pluto. To help Mickey in his journey, he can jump on or throw things (including stunned creatures) at his adversaries. In addition to employing these standard methods of attack, Mickey can become a wizard, a fearless firefighter, or a mountaineer. These costume changes give him the ability to release bolts of magic energy, spray powerful streams of water, and scale perilous mountains. Once Mickey acquires a costume, he can put it on or take it off any time he wishes.

An updated version of The Magical Quest starring Mickey Mouse (a side-scrolling Super NES title), Disney's Magical Quest Starring Mickey & Minnie includes new Game Link Cable multiplayer features. Also, players can link their GBA systems to a Nintendo Gamecube and exchange items with Disney's Magical Mirror Starring Mickey Mouse characters.