Destro returns to Cobra base and seizes control of the operation from the Commander. The now-captured Scarlett and the slave girl organize a slave revolt. Duke's memories under sensory deprivation lead the Joes to the Cobra base where a final battle takes place. Cobra Commander is captured and taken to prison, but Destro escapes. The battle is over but not the war!
Flint and Mutt, stranded by the weather dominator, hire Shipwreck to ferry them out of Cobra territory. Meanwhile, the Joes develop an energy mirror to fight the dominator's attacks, but Destro smashes them with a hailstorm. During the battle, Destro's weapon breaks, and the three pieces scatter over the globe.
Cobra briefly attacks a Joe shuttle launch long enough to load it with its own forces. Shipwreck and Snake Eyes are lost in Cobra territory, and Zartan uses the shuttle to commandeer a space station and destroy Joe Headquarters from space. Meanwhile, Cobra Commander reveals a plan to deprive most of the world of electricity.
Cobra kidnaps a French scientist named Dr. Emil Mettier, and Zartan replaces him before he arrives at the World Wide Defense Center to complete their database on terrorism. Spirit is suspicious of the doctor, and when he investigates, he is confronted, then captured by Storm Shadow. Freedom escapes, and leads Lady Jaye, Recondo, Doc, Gung-Ho and Stalker back to the Defense Center, only to discover that Zartan has replaced the doctor and has set up a bomb. While the Joes search for the bomb, Gung-Ho locks Zartan in a prison cell in plain view of Zartan's countdown watch, which unbeknownst to Zartan, Gung-Ho has set it two minutes ahead. Zartan is fooled, and reveals the location in time for the bomb to be disarmed. Zartan escapes, and Spirit and the real Dr. Mettier are saved from death by laughing gas by Storm Shadow. Cobra launches one more futile attack, the Joes counter it, and all's right with the world.
Mutt, Junkyard, & Ripcord are kidnapped by Cobra, so that the evil scientist, Dr. Lucifer, can test his new invention, High Freq, a device which controls the minds of animals and insects, on Junkyard. Cobra use it to gain control of an army of animals to take over the world, and send Junkyard hunting after Mutt. In exchange for High Freq, Cobra agrees to break Dr. Lucifer's love, Dr. Attilla, out of jail. GI Joe learns of this, and has Scarlett pose as Attilla, but it's obvious to Lucifer she is not Attilla, and Scarlett is captured. Snake-Eyes and Spirit come to the rescue, using Timber and Freedom to sneak into Cobra's jungle castle and rescue Ripcord and Scarlet, and stop High Freq.
An ancient Babylonian manuscript on secret potions is stolen from the British Museum. Meanwhile, Zartan leads Cobra troopers on a search for a rare fungus to help create an irrestible perfume to make a famous Greek shipping tycoon fall prey to the Baroness' charm and put his entire task force in Cobra's control.
Cobra makes a generous donation to the Joes' toy drive: a battalion of Cobra troops, miniaturized to look like toys. Once inside Joe Headquarters, the Cobra forces sabotage the defenses, open the gates, and let the rest of the Cobra forces inside. The Joes have to use Cobra's vehicles to stop Cobra's attack on the city using the Joe's own vehicles.
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?
Cobra uses a shuttle to steal all communication satellites. That means the only television network available is the Cobra Network Television which provides programs promoting their social messages such as Father's No Beast and new endings to classic movies. G.I. Joe first send three Joes up in Skystrikers powered by rocket boosters to take out Cobra's satellite. They discover that it is really a space station and are blasted back down to earth. Next they have a space training program to select a group of Joes to go back up. Their Skystrikers are destroyed again by the Space Station, but the group sneaks inside. Being better trained, they defeat the Dreadnoks and destroy the Space Station, escaping in a Cobra Shuttle, thus saving the wonderful world of television.
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!
A surprise attack by Cobra, using the new BATs, reveals that the Joes have gotten sloppy. General Hawk asks Sergeant Slaughter to help whip the team back into shape. Meanwhile, a series of dreams prompt Dr. Mindbender to concoct a plan to build a new Cobra leader from the DNA of long-dead conquerors. A package downed Night Raven reveals that Zartan has been asked to expand his team of Dreadnoks so he turns to his siblings, Zandar and Zarana for help, and the Joes investigate and discover the plan, only to be cornered by Thrasher and his Thunder Machine.
The Joes send teams out to guard the tombs on Zartan's list, but each team is defeated in turn: by Zarana in Egypt, the Crimson Twins in Paris, the Dreadnoks in the Yucatan, and the Baroness in Transylvania. Duke's team and the Oktober Guard are in a standoff with BATs while defending the tomb of Ivan the Terrible.
Cobra takes DNA from the tombs of Ivan the Terrible and Alexander the Great. Sergeant Slaughter retrieves a DNA pack from Cobra's raid on Sun Tzu's tomb, and from it the Joes surmise that Cobra is building a new breed of soldiers. Dr. Mindbender intends to use Slaughter's DNA as a replacement, and so feigns defeat as a ploy to retrieve the sarcophagus of Genghis Khan and capture Slaughter.
Cobra Commander sabotages Dr. Mindbender's first experiment, and it rises as a hideous monster. Sergeant Slaughter briefly escapes, then is recaptured but manages to destroy his DNA sample. The second attempt is successful, and Serpentor is created. Meanwhile, a Joe search party is sent to Cobra Island to rescue Slaughter and learn more about Cobra's plans.
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.
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...
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.
Cobra takes advantage of General Hawk going to a NATO meeting in Europe and infiltrates the Department Of Defense's computers and promotes Lifeline, Dial Tone and Shipwreck (who's not even in the army) all to the rank of Colonel. The three can't cooperate and are not quite officer material which creates utter pandemonium at G.I. Joe Headquarters. Cobra capitalizes on the situation and attacks a research lab near the Joes' base. The Joes are defeated easily and fall back to Joe HQ. Hawk arrives in the nick of time and organizes a counter offensive, pushing Cobra back.
All of the Joes are having nightmare involving a huge snake attacking them. At first they feel that it is due to the stress of the situation. As the nightmares continue, it begins to affect the Joes performance fighting Cobra. In fact, Cobra is controlling the Joes' dreams in an effort to disable them...
A group of Joes are attending Lifeline's sister's wedding while other Joes are at a nearby weapons depot testing new armor. The Dreadnoks are able to attach small receivers to the back of the Joes' necks and capture Roadblock. Dr. Mindbender uses an organ to send signals to the receivers that controls the Joes emotions...
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 Commander tries to communicate with the creature in the pit at Destro's ancestral home in Scotland and fails. Meanwhile, Dial Tone is discharged from the Joes and is hired to work on a communications project that turns out to be communicating with the creature. Flint is sent to spy on Dial Tone in disguise. Dial Tone gets the machine to work and Cobra Commander tells it to destroy Serpentor... (Destro's "ancient chant" is reversed speech, revealing a humorous message poking fun at the then-relevant backmasking concern when played in reverse.)
Slipstream in his Conquest intercepts a Cobra message, which contains an important command code. A squadron of Night Raven are sent after him. He and one of the Night Ravens crash land on an remote island Cobra base. The Stratoviper, a lady named Raven, is injured and not very friendly towards Slipstream. But when BATs land on the island and start firing on both of them, the are forced to team up and enter the abandoned Cobra base, with Doctor Mindbender watching...
The Joes are highly annoyed by Cross Country's country music are glad when his tape deck is destroyed during a Cobra battle. When his new tape deck is stolen back at HQ, he intends to find out what's going on and sets a trap. He spots a robotic rat stealing the tape deck and he follows it to a Cobra meeting of the Coil, a group against Serpentor lead by Cobra Commander...
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.
The Joes are on vacation at Volcania, also known as 'Club Joe', also on the Island of Volcania is General Hawk, who has been reassigned because his superiors believe he is too old. Cobra launches an attack on Volcania and assumes control of the Island, Destro has created new weaponry which Cobra Commander threatens the world with. When they do not meet his demands, Cobra Commander becomes angered and fires on the California River bridge...
The United Nations do not believe Cobra Commander really destroyed the bridge, and send a fleet to Volcania. General Hawk rescues the Joes and they attack the Cobra Command centre hidden within the Volcano, the command centre is destroyed and takes Destros space gun weapon with it. Cobra Commander and his troops pursue the Joes until reinforcements and the UN fleet arrives, allowing the Joes victory once more.
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'...