When The U.S. military prepares to launch their satellite into orbit, Cobra develops the ultimate weapon known as the M.A.S.S. device, planning to steal the satellite. G.I. Joe is called into action, their leader Duke has Scarlett, Snake Eyes and Stalker test the satellite installation's security. But while in disguise, the Baroness tags the satellite with a homing device, causing Cobra to use their device to transport forces stealing the satellite. Meanwhile, Duke is captured during the transport and the rest of the Joes must rescue him.
The Joes begin the race to acquire the elements necessary to build their own MASS device. Cobra kidnaps Duke, using mind control device to put him in a gladiator type environment called the Arena of Sport. After Cobra discovers the Joes are searching for radioactive crystals, the race begins. Snake Eyes sacrifices himself to save his friends, acquiring the crystals while he is poisoned from the radioactivity. Duke is able to break the mind control device and is rescued by MEDEVAC.
The Joes and Cobra vie to find the heavy water element. Mysterious underwater tube worms cause both teams to agree to a cease fire to thwart off the worms, allowing both teams to successfully recover the heavy water. Snake Eyes struggles to remain alive in a snow storm and is suffering from radioactive poisoning. He manages to save a wolf (Timber) who becomes his makeshift pet. The pair are rescued by a hermit who cures Snake Eyes of his poisoning and injuries. The Joes are overjoyed to see their comrade alive and with the crystals. However, his canister was booby trapped by Cobra; causing poison gas to flood the air. This episode includes the introduction of the second female G.I. Joe team member, Cover Girl.
After Covergirl and Timber save the lives of the G.I. Joe team, the Joes continue to search for a way to stop the Cobra terrorist organization. Both forces begin missions to retrieve the third element, a meteorite buried in a volcano. The Joes try to lift the meteorite, but are thwarted by Cobra, led by Destro, who causes the volcano to erupt, ejecting the meteor. But both forces obtain the third element. The Joes have all three elements and want to attack Cobra, but Duke has no recollection of where Cobra Mountain is located.
Cobra attempts to destroy New York City, but the Joes counter it with their new MASS device. The Joes notice the ring Duke gave to the slave girl was a homing device, and they teleport to Cobra Mountain. The Joes arrive at Cobra headquarters to launch their assault. Destro turns the MASS device to the direction of earth's core in order, disintegrating it. Cobra Commander, in panic, enlists the help of the Joes to stop the device. After successfully destroying the device, Cobra Commander is arrested and Destro escapes.