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

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!

Cobra discovers an Asian tree sap that brainwashes people, and uses it to enslave the native population. Leatherneck must care for four orphans while the other Joes try to prevent Cobra from marketing the sap as chewing gum.

When an orphanage is accidentally damaged during a battle, Shipwreck and other members from G.I. Joe volunteer to help repair it. While doing so, Shipwreck is dragged into telling the children a fairy tale...a typically cockeyed Shipwreck extravaganza!

Bree Van Mark, a cute wealthy woman, develops a crush on Lifeline after he rescues her and her father from a sinking yacht during a battle between G.I. Joe and Cobra. Lifeline discovers that Cobra is after Bree's father, a wealthy industrialist whose holding include a defense company. But the Joes think that Bree is working for Cobra since some of her gifts, including a gold plated helicopter, have backfires. She flies off in a Tomahawk taking Lifeline with her. They head to a cabin in the Rockies and are followed by Cobra. Lifeline, who is a pacifist, must fend off Cobra until the rest of the Joes arrives.

Cobra stages a telethon to raise money for a computer virus that will bring down all the computer systems in the world, as the Joes try to rescue Sci Fi and Lifeline...

Leatherneck attends graduation ceremonies at a new academy and discovers it run by former enemy Buck McCann, who is loyal to Cobra. Leatherneck must foil McCann's plan to destroy Parris Island Marine Academy.

Madame Vail (voice- Mary McDonald Lewis) agrees to sell her youth transference machine, which makes people young (and beautiful), in return for kidnapping some of the world's top models, who's youth and beauty will be transferred to the machine's user. One of these models is Low Light's sister, Una...

The Joes visit an arctic region where Icebergs Girlfriend is collecting samples of animals tissue for her Uncles research at the Tropadome. Icebergs goes to the Trapadome only to be captured by Doctor Mindbenders new mutant animal army...

International superspy Matthew Burke volunteers his services in helping the Joes transport nerve gas to a safe facility.

Cobra steals Madame Versalles youth treatment. The Joes try to figure out why and that leads them to the Ageless Care Spa, where lady Jaye, Mainframe and Dial Tone are turned into seven year olds...

Sergeant Slaughter accompanies Sci-Fi to a science fiction convention, where Dr. Mindbender recruits a handicapped scientist to repair his latest weapon. Mindbender's false promises to enable the scientist to walk again lead him to walk all over his brother.

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.

G.I. Joe is acting as the Peace Corps helping a poor village, when they met journalist/cameraman Leonard Michaels aka Scoop who joins the Joes. Cobra attacks a monastery to get the secret to the Dragonfire, a mysterious energy in the earth. Destro dumps the Baroness for Zarana, so Baroness plots with Gnawgahyde to return Cobra Commander to human form to get revenge. Scoop turns out to be a Crimson Guard commander spying on GI Joe...

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.

Night Creeper Leader is hit on the head during a battle with the Joes in Egypt and begins to believe he is the reincarnated Pharoah and attempts to take over Egypt...

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