In a clip show, General Hawk advises the audience what it takes to become a GI.Joe.

Wet-Suit and Leatherneck have never, ever got along but their heated rivalry must take a backseat when Serpentor begins collecting artifacts from his former lives to gain power, and Leatherneck is poisoned trying to stop him. Wet-Suit has to prove he doesn't have any hard feelings for Leatherneck, as he and Lifeline risk their lives trying to recover an antidote from Serpentor's blood.

A civilian's home is destroyed during a battle between G.I. Joe and Cobra, and he breaks into G.I. Joe Headquarters to seek revenge against Cobra.

A Joe transport plane is caught in a storm, forcing the pilot to ditch his cargo, a valuable Mauler tank, over the desert. Dusty and Footloose volunteer to stay with the tank until it can be retrieved. They inadvertently parachute onto a Cobra proving ground and discover the evil organization's latest innovation: a metal alloy that's impervious to any conventional weapon! With tanks and planes constructed of this alloy, Cobra could attack the Joe team – or anyone else – without fear. With a battalion of Cobras hot on their heels, can Dusty and Footloose survive the track across the hostile desert to warn the Joes?

G.I. Joe is placed under the command of a new computer, Watchdog, which directs Joes to Cobra targets. The computer is under Cobra's control, being used to spread Joe forces thin and leave headquarters vulnerable to attack.

The Joes join forces with a Soviet operation team called ""The October Guard"" to save the world from what seems to be an invasion from outer space. But what is it about this flying saucer threat that seems so daunting? Do the space creatures really exist?

When the last surviving heir of the Russian Imperial Alaskan Colony Company shows up and claims to own Alaska, the Joes suspect it is a Cobra plot to wrench away America's largest state. The only way to disapprove the claim is for the Joes to go to Alaska and find the colony's Imperial Seal. Three problems: the seal has been missing for over a hundred years, the Russians are looking for the seal so they can reclaim Alaska, and Cobra is determined to stop them both!

There is a Joe/Cobra battle over the Suez Canal when a spacecraft flies overhead and drops a glowing coil. When Joe and Cobra teams are dispatched to investigate, they are sent back to Ancient Greece...

Wet Suit, Leatherneck, Dial Tone and their dates attend the grand opening of a trendy new night club. The club turns out to be on a Cobra rocket and is sent into orbit around earth. Serpentor demands that Dr. Mullaney surrender himself and his nitrogen fuel engine over to Cobra or they will detonate the club. Wet Suit goes outside the club and with Leatherneck's help, disables the bombs. Meanwhile, Dr. Mullaney surrenders to Cobra. The Joes use the Nitrogen engine to bring the Club back to Earth and Dr. Mullaney escapes, when all of the Cobra jets with the new engines crash thanks to the unstable Nitrogen fuel, turning all the Cobra jets into fire bombs.

Cobra has a map showing the locations of Dragonfire around the world, and the Joes and Cobra battle over one of the locations in a mountain. Baroness and Gnawgahyde use the Dragonfire to DNA convert Cobra Commander back into human form. The Joes manage to get inside the mountain base, but are flooded out...

Next location is a jungle temple in South America, and there's three factions: Serpentor, the Joes, and Cobra Commander. Scoop finds out he was tricked into joining Cobra and turns against them. But the Joes discover he's a Cobra. Cobra Commander uses the Dragonfire to turn monkeys in Ape Warriors that attack the Joes...

Scoop returns to Cobra to try to defeat them. Gnawgahyde steals a Conquests and blasts the Joes. Cobra Commander starts fusing animals with vehicles and creates Python Patrol. Serpentor is defeated and fused with Gnogahide's pet iguana. The Joes return to base while Low Light stays behind. Destro dumps Zarana for the Baroness...

The final location is a mesa. Cobra links all of the Dragonfire bases together through their satellite to create an energy weapon and to supercharge their vehicles with the Dragonfire energy. Finally the Joes have their own Dragonfire after Freedom finds a Native American man who knows how to active it. Scoops sends the Joes the frequency to disable Cobra's Dragonfire and causes a chain reaction that destroys all of Cobra's Dragonfire bases.

Metal Heads Grandmother comes to visit, who believes he is the leader of Cobra, much to Cobra Commanders disgust...

The Joes play a football match against Cobra, with Sgt.Slaughter as the ball...

Cobra Commander disguises himself as a new superhero named Serpent Man in an effort to humiliate G.I Joe...

When G.I Joe are told they are exceeding government funding they have to report to The Battle World proving grounds to learn how to fight cost efficently under the supervision of Dr.Carday who is secretly Zarana in disguise. Meanwhile Cobra Commander plans to steal a new weapon named 'The General'...

Cobra Commander tries to make a break into the world of stand up comedy by impersonating a famous comedian while planning a trap for the Joes...

At the unveiling of a new tunnel between England and France, Cobra Commander kidnaps the Queen of England and steals the crown jewels, proclaiming himself King...

Cobra replaces General Hawk with an android replica...

Cobra Commander believes a hidden city under the sea will make him rich, but both the Joes and Cobra find out it holds a more dangerous secret...

Cobra Commander attempts to lure Storm Shadow back into Cobra...

Cobra Commander tries to convince the world he has gone straight and opens his own theme park...

Cobra takes control of a school in the hope of training new Cobra recruits from a young age.

Metal-Head goes to his high school reunion in an effort to get a secret armor formula for Cobra...