The story follows Bart's quest to prevent the Space Mutants' invasion, with each level requiring him to collect specific items, such as purple objects or brown coins left behind by the aliens. Collecting these items allows Bart to defeat the aliens' bosses, including characters like Nelson and Sideshow Bob.
Gameplay involves navigating through five levels, using various methods to get rid of the objects sought by the Space Mutants, such as dyeing them red or playing a trick on Moe to make him leave his bar. Bart also collects coins that can be used to solve puzzles and unlock new items.