One day, Wario's plane stalls and crashes while he is flying over the woods. Uninjured, he spends the rest of his afternoon wandering amongst the trees and underbrush until he stumbles upon a mysterious cave. Inside the cave, he discovers a magical music box and is suddenly sucked into it. There, a mysterious figure informs Wario that he had once ruled the world inside the music box, until an evil being sealed away his magical powers in five music boxes. In exchange for freeing it, the being promises to send Wario back to his own world and let him keep any treasure he finds. Enticed by the thought of returning to his own world with a cache of treasure, Wario departs on his quest, in search of the music boxes and the many treasures of this mysterious land.
After collecting all the music boxes, Wario returns to the mysterious being's temple. The music boxes play a medley together that frees the being, revealed to be Rudy the Clown. It transpires that Rudy is in fact the villain and had been imprisoned, although not before turning the music box's inhabitants into monsters, who had been attacking Wario simply to try to stop him from freeing the evil clown. After Wario defeats Rudy, he is met by the inhabitants of the music box, now restored to their former selves. They thank Wario and transport him back to his own world, along with the treasure that he has collected, as promised.