Commander Keen 6: Aliens Ate My Baby Sitter! is a platform game, the sixth in the Commander Keen series as a whole.

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.

The levels are full of enemies, including the club-wielding Blooguards, the Flects which can reflect Billy's shots with their teeth, and Nospikes which charge at him in hopes of impaling him. There are also many deadly hazards. If Billy gets shot or touched by an enemy, or falls into a pit or touches something hazardous, he dies and loses one life.

Thankfully, Billy can stun most enemies with his raygun. He also carries a pogo stick which allows him to jump very high. Other items to find include: ammo, gems that are needed to open locked doors, bonus items which give score, bird-like "Vivas" (100 of them give an extra life) and the rare Queen Viva which gives an extra life.