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In the first episode, "Marooned on Mars", eight-year-old Billy Blaze, a child genius, builds a spaceship (the "Beans with Bacon Megarocket") and puts on his older brother's football helmet to become Commander Keen. One night while his parents are out of the house he flies to Mars to explore; while away from the ship the Vorticons steal four vital components and hide them in Martian cities. Keen journeys through Martian cities and outposts to find the components, despite the efforts of Martians and robots; the final component is guarded by a Vorticon. Keen returns to Earth—discovering a Vorticon mothership in orbit—and beats his parents home. In "The Earth Explodes" he travels through the mothership and disables its weapons, at the end discovering that the Vorticons are being mind-controlled by the mysterious Grand Intellect, who is actually behind the attack on Earth. In "Keen Must Die" he fights through the cities and outposts of the Vorticon home planet to reach the Grand Intellect, who is revealed to be his school rival Mortimer McMire, who he then defeats.
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