Five aliens - Candy, Etno, Gorgious, Stereo and Bud - crashland on Earth, and hide out in an abandoned house while they repair their spaceship. In the meantime, Dr Sakarin, an evil alien-collecting scientist has found out about them, and sends out his evil henchman Bolok to capture them. The player alternates between controlling each of the five aliens, and must help them escape.

Stupid Invaders is based on the French and German animated TV series Space Goofs (also known as Home to Rent). The player interacts with the environment in a point-and-click fashion. Up to six items can be carried simultaneously and used to solve puzzles. Many actions lead to instant death of the protagonist, often graphically depicted and used for the humorous effect of cartoon violence.