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Mouse Banjo is the transformation found in Cliff Farm after beating Klungo for the first time. In this form, Banjo can chew through switches and other objects, as well as fit through small holes. If Mouse Banjo enters water in this form, he dies.

His chewing move is used to free the breegulls in Breegull Beach. The mouse can also enter the sand castle in Bilge Haven (an area within Spiller's Harbor) and also the block of ice near Mumbo's Pad in Freezing Furnace. This is the first transformation in the game.