| ShortSummary
| - On the Island of No Return, Spirit saves Stormshadow from drowning while escaping from an underground river. In return for his heroism, Stormshadow allows Spirit to keep the fragment. Flint, Lady Jaye, Snow Job, Spirit, Gung-Ho and Shipwreck head to the North Pole to retrieve the third fragment, The Laser Core, and are opposed by Destro and Zartan. Zartan finds the 3rd fragment, and he blackmails the Joes and Cobra that the final fragment will belong to the highest bidder.
- Both forces begin missions to retrieve the 3rd element, a meteorite buried in a volcano. The Joes try to lift the meteorite, but are thwarted by Cobra, led by Destro. Destro causes the volcano to erupt, ejecting the meteor. Both forces obtain the 3rd element. The Joes have all 3 elements and want to attack Cobra, but Duke has no recollection of where Cobra Mountain is located.
- Zartan broadcasts an unsecure message to the Joes and Cobra offering to bargain for his particular fragment. Both sides trace his call to an amusement park. Cobra captures Zartan, and now they possess all the pieces of the Weather Dominator since Stormshadow sneaked into Joe HQ and stole their fragment. Duke and company raid the Cobra Command center as Roadblock uses vines to attack Destro. The Joes are able to destroy the weather dominator, rescue Duke and company and apprehend Cobra Commander. Destro and Zartan escape on a hang-glider.
- Cobra Commander regains control of Cobra in a coup over Serpentor
- Cobra Commander is returned to Human form by Baroness
- 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 make-shift 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.
- Serpentor seizes control of the Dragonfire
- The final battle between GI Joe and Cobra
- Cobra and the Joes head for “The Palace of Doom”, an alleged cursed Aztec temple, to retrieve the first fragment, the ion corrolator. Cutter, Wild Bill and Spirit along with Doc, Torpedo, Clutch and Rock 'n Roll head to an unstable island in the Pacific called the Island of No Return to retrieve another fragment, the Hydro Master, and are opposed by the Baroness, Firefly and Zartan. The Joes retrieve the corrolator, but they lose the fragment to Cobra during an earthquake.
- The U.S military prepares to launch their satellite into orbit. Duke has Scarlett, Snake-Eyes and Stalker test the satellite installation's security. A disguised Baroness tags the satellite with a homing device. Cobra uses the MASS device to transport forces to steal the satellite. Duke is captured during the transport.
- Cobra attacks G.I. Joe convoy and steals a high-powered experimental laser. During the battle to protect the laser, both Duke and Snake Eyes are captured by Cobra agents. Once back at Cobra's base, Destro uses the laser to complete his latest weapon... the Weather Dominator. When Flint and the other Joes launch an air assault and rescue mission, Destro uses the device, and it's stormy skies ahead for the Joe team.
- Cobra Commander finds the Dragonfire energy and Scoop finds out Cobra lied to 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. 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.
- Cobra attempts to destroy New York City, but the Joe's 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 HQ to launch their assault. Destro turns the MASS device to the direction of earth's core in order, disintegrating it. Cobra Commander, in panic, enlist the help of the Joes to stop the device. After successfully destroying the device, Cobra Commander is arrested and Destro escapes.
- Cobra Commander's has Duke and Snake-Eyes fight each other in a gladiatorial combat in his Arena of Sport. Cobra plans to assault Washington D.C., but Duke and Snake-Eyes send a Morse code to the Joes. The Joes successfully defend D.C., but destroy the weather device by splitting itinto three pieces scattered globally. Weather patterns all over the world are in havoc; G.I. Joe and Cobra begin expeditions to recover the shattered device.
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