Molly, the babysitter of Billy "Commander Keen" Blaze (an eight-year-old genius) has been kidnapped by the Bloogs from the planet Fribbulus Xax, for purely gastronomical purposes. Keen must set out to Fribbulus Xax to save her!
The game begins with a top-down map of the Fribbulus Xax. This is the level select screen, where Billy can walk around and the player can choose the next level they want to enter; however, some places on the map require the player to find specific items (such as a grappling hook) to get through. On each level, Billy has to make his way to the exit. Once a level is completed, Billy ends up back on the overhead map.