Zartan and Cobra seize the Delta Space Station and destroy G.I. Joe headquarters. Shipwreck and Snake Eyes are lost behind enemy lines while Cobra Commander reveals his plan to deprive the world of electricity.
G.I. Joe sets up temporary headquarters on the U.S.S. Flagg. On the Delta Space Station, Dusty, Buzzer and Mutt work to warn the Joe team about Cobra's plan to plant cubes at strategic locations in order to create the pyramid of darkness.
G.I. Joe sends teams to different parts of the world in order to stop Cobra from planting their electronic cubes. Meanwhile, Shipwreck and Snake Eyes continue to lay low behind enemy lines.