During a joyride in his biplane, the engine blows and Wario crashes into the woods. It's here where he finds a hidden cave with a magic Music box. Before he can say "I hate Mario", the box pulls him inside and into a room with a dark figure, who strikes a deal with him. Find all of the missing Music boxes and he can leave. And any treasure he finds he can keep.

Much like Wario Land II, Wario can't die from any attacks by the enemy. However he can change form after certain attacks, which can both help and halt his progress in each level. New forms of Wario include Invisible Wario and Ball of Yarn Wario (an un-controllable ball of yarn, with Wario inside).

Also, basic attacks such as swimming and the butt stomp don't become available to Wario until after completing a certain amount of levels, meaning you have to go back to completed levels to access other areas full of loot.