In the game, you control a character named Balloon Man, who is a member of the sky patrol. Prior to the start of the game, he battled and defeated the pirate boss Oiram Repus (interestingly spelled Super Mario backwards) and put him and his henchmen all in jail. The boss managed to escape and free all of his henchmen, who tore the map (to where Oiram is) up into small pieces and spread them across the land in balloons. The balloons all floated up to Trip-Sky, and now the sky patrol must find them all and gain the contents within so that they can recreate the map and find the boss to place him back in the Federal Prison.