The Pyramid of Darkness was a weapon system created by the Cobra organization to deprive the Northern Hemisphere of Earth of electrical power. Cobra's plan is to position four giant "control cubes" at strategic points around the world. The cubes, designed with sophisticated electrical components and defense systems, will receive energy beams from the captured GI Joe space station, Delta, which Cobra has seized control of in orbit above the North Pole. As each cube is placed and activated, a new face of the Pyramid is formed. Once all four sides are completed, the sky darkens and no electrical power source or equipment that operates electrically can function underneath its range.
GI Joe sets up their new, temporary headquarters aboard the carrier, the USS Flag. They engage Cobra's military forces at each cube location around the world in dangerous conditions but are unable to stop the Pyramid's initial activation. Aboard the Delta Station, the Joes have been forced into hard labor. Cobra forces, lead by Zartan and the Dreadnoks, have been keeping the artificial gravity low to suppress any rebellion and have also brought along mutant creatures that grow into monstrous, fire-breathing beasts when a special whistle is sounded, a further deterrence. Dusty and Mutt are able to alert Joe command to the situation. They eventually hatch a plan to fight Zartan and his crew and restore gravity to the station. They force a temporary deactivation of the Pyramid, forcing Cobra Commander to order Destro and the Baroness to construct a lower-powered Pyramid to buy time.
The Joes find themselves in a battle to both stop Cobra and locate the Pyramid's self destruct controls. Finding themselves in enemy territory, Shipwreck and Snake Eyes elude Cobra forces and are able to steal information about the Pyramid and the cubes from Cobra's production facility in Enterprise City. Hiding in a Cobra-frequented nightclub, they ally themselves with a singer named Satin, who provides them with disguises and sneaks them out of Cobra territory. They make it back to Joe HQ and are able to pass on the info about the Pyramid, including the self-destruct mechanism to deactivate it permanently.
At a site for one of the cubes, on the slopes of a high-altitude mountain range, Alpine and Bazooka are separated from the team that fights Cobra. They find Quick Kick, a sharp-witted martial arts expert who was shooting an ad for candy bars when his production company left him behind. They steal aboard a Cobra HISS tank that takes them back to Cobra's hidden temple. They eventually escape and make it back to Joe HQ, revealing the location of the temple.
The Joe forces launch a counteroffensive on Cobra Temple. They are immediately pinned down by a large sonic weapon which Alpine, Quick Kick and Bazooka destroy by yodeling over their vehicle's speaker system. The renewed attack is successful and the Temple falls. They find the destruct mechanism for the Pyramid, throw the switch and the Pyramid is permanently destroyed.