DaGoulian, a philosopher, has come up with a disturbing theory: he believes that to save the good, the world must become more evil. He created special drums using science and alchemy, allowing him to control "skeletism" power. Using this power, DaGoulian brings people's skeletons back from the dead, building an army to fulfill his crazy plan. However, one of these skeletons had a pure heart, and instead of being affected by evil skeletism, he is reanimated with its blue version, allowing him to think for himself and resist DaGoulian's orders. The skeletal rebel must fight for survival and eventually find a way to stop DaGoulian's madness.
Mr. Bones is an action game that features numerous stages. Each stage has a unique goal and introduces new gameplay styles. Some stages are longer platform levels, while others are short timed sequences. Many of the stages involve avoiding hazards or enemies, as well as completing tasks within a certain time limit. The skeletal protagonist, Mr. Bones , usually has no offensive powers. When damaged, he loses limbs and bones, affecting his movement and speed; he may even be left with just his head and neck hopping on the ground.