Wario Land 3 tells the story of Wario 's journey through various worlds in search of the missing music boxes. After his biplane crash, Wario is transported into a mysterious world where he must find all the missing Music boxes to escape. Along the way, he can collect treasure and use his unique forms to overcome obstacles.
The gameplay of Wario Land 3 is similar to its predecessors, with Wario able to move freely through levels without taking damage from enemies. However, Wario can transform into different forms, such as Invisible Wario and Ball of Yarn Wario, which can aid or hinder progress in each level. Certain attacks, like swimming and the butt stomp, are initially unavailable to Wario but become accessible after completing a set number of levels.