Dr. Robotnik has hatched a plan to ensure that no fun or music remains on Mobius. To do this, he kidnaps the jolly citizens of Beanville and stuffs them into a giant roboticizing machine called the Mean Bean-Steaming Machine to turn them into devious little robot-slaves. Across Beanville, Beans disappear and are sent to the Mean Bean Machine. The player sets off on a daring adventure to defeat Robotnik's minions and stop Robotnik. The game ends after a face-off with Robotnik, in which the Mean Bean Machine is destroyed and the Beans are freed.
Robotnik's nemesis, Sonic the Hedgehog, is never mentioned throughout the game to rescue or help the player.