The game features the return of Wario's nemesis, Captain Syrup. Early one morning, she and a few of her soldiers, the Pirate Gooms (Spearmen, which are holdovers from Wario Land; several different levels deal with defeating a giant Spearman), sneak into Wario's Castle and cause havoc. They steal his precious treasure, set off his giant alarm clock, and leave the tap running, flooding much of his castle. After Wario wakes up and figures out what's going on, he gives chase across the surrounding lands.

The game is noteworthy for its branching paths. By finding hidden exits in some stages, the player can change the direction of the game's plot (loose as it is) and uncover different endings, as well as find more treasure.

This is the original Game Boy version of the game, though a Game Boy Color remake was released about one year later.