Cobra seizes control of a new satellite for use with a new transportation device, and Duke is captured in the attempt. The G.I. Joe team learns that they must build their own device to defeat Cobra.
The Joes travel to the arctic to retrieve rare minerals to fuel their MASS device, but Cobra ambushes them, and Snake Eyes is presumed dead. Duke manages to escape the Cobra base with the help of a slave girl, but he is injured and cannot remember the base's location.
Snake Eyes returns home with the help of a wolf and a blind man. The Joes and Cobras battling for undersea elements must join forces to escape giant tubeworms on the ocean floor.
G.I. Joe tries to throw off Cobra with a false surrender while mounting a mission to the Ring of Fire for the third element. Destro sabotages the operation but is pursued by Scarlett.
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!
A Cobra attack on a Joe convoy results in the capture of Duke and Snake Eyes and the theft of a laser core which Destro uses to power his new weapon, the Weather Dominator. Meanwhile, Cobra Commander is briefly captured but rescued by Zartan.
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.
As Flint, Mutt, and Shipwreck return to Joe Headquarters, the Joes and Cobras head to the Island of No Return and the jungle Palace of Doom to retrieve parts of the weather dominator.
As G.I. Joe and Cobra race to retrieve the three parts, Zartan ensures that each side acquires one piece, and then steals the laser core at the Roof of the World.
Cobra steals the Joes' piece of the dominator and assaults Zartan's base. Now in possession of all three pieces, Destro seeks to rebuild the weather dominator. The Joes locate the Cobra Temple and attack it.
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.
With G.I. Joe headquarters nearly destroyed, the Joes establish a temporary base on the USS Flagg. Joes on the space station try to warn the team of Cobra's plan to plant cubes at strategic locations to create an electricity-inhibiting pyramid over the northern hemisphere.
Quick Kick joins Alpine and Bazooka, and the Crimson Twins turn the tables on Cobra Commander by taking control of the space station and the Pyramid of Darkness.
As the Cobra leaders struggle for control of their organization, Quick Kick and Shipwreck lead the Joes in an assault on Cobra forces to destroy their pyramid-creating abilities.
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.
Extensive Enterprises uses biker gangs to terrorize Red Rocket diners, then buys them back at a lower price and replaces the diners' rocket props with real rockets. But Roadblock's family, unaware of EE's connections to Cobra, refuses to sell their restaurant.
When Cobra uses a tractor beam to steal a spy satellite recently placed in space by the Joes, Breaker forces the satellite to crash in the jungles of Africa, but a tribe of hominid Primords complicates Joe and Cobra's efforts to recover the technology.
Cobra attacks crucial oil derricks, pipelines, and tankers, seeking to control the world's fuel supplies. But G.I. Joe use Cobra Commander's remote-control attacks to pinpoint his location.
Cobra kidnaps scientist Dr. Shakur in order to harness the energy of Earth's core and cause volcanic eruptions, but the Joes work through a number of traps to raid Cobra's jungle base and destroy Cobra's newest weapon.
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.
Flint, Dusty, Bazooka, Alpine, and others have to break into a temple to stop Cobra from its next plan to take over the world. When the temple turns out to be a fun house with obstacles of death, the Joes have to find their way to Cobra Commander and save the day!
Investigative reporter Hector Ramirez believes that Cobra is not a real threat and that G.I. Joe is a drain on taxpayers' money. But Shipwreck takes him on an unauthorized mission into Cobra territory to prove their danger.
A Crimson Guard steals a container filled with experimental rocket fuel, causing plants to grow to gargantuan sizes. Destro convinces Cobra Commander that the plants could be used in combat. Harvey 15 Bullock 6
The Joes travel to the arctic regions at the top of the world in order to stop Cobra from using the Aurora Borealis to melt the ice and flood coastal cities around the world.
Cobra attempts to cripple the Joes from within by replacing leaders and committee members with artificial beings known as synthoids. The synthoids cut G. I. Joe's budget and eventually order the team to disband.
Cobra Commander recruits an elderly Gypsy woman to use three small artifacts, which allow them to command three ghosts to attack the Joes. The Baroness and a phantom World War One pilot help the Joes recover the artifacts.
Cobra backs a candidate for mayor and uses street thugs to intimidate voters and drum up public sympathy for Cobra's would-be mayor. The gang turns on Cobra when a brother of one of the youths is nearly burned in a fire.
Flash, Airborne, and several other Joes discover that Cobra has amplified the psionic powers of some civilians for use as living weapons; one of the captives is Airborne's telekinetic brother.
Cobra steals the gold stored at Fort Knox and begins moving it out with a bullet train. When the Joes' equipment is destroyed in a surprise attack, they must use horses to stop the train.
Cobra purchases a dude ranch through one of its dummy corporations, intending to control a nearby solar power station. G. I. Joe travels to the ranch to flush out the Cobras.
Quick Kick's girlfriend Amber breaks into G.I. Joe Headquarters with the intent of joining the team, and Cobra Commander steals a prototype laser device to carve his likeness on the moon.
A Cobra spy steals a deadly bacteria along with an experimental growth serum and accidently creates a living, growing and monstrous terror. G.I. Joe must use an orchard of apples to destroy it.
The Baroness discovers a conch shell whose song hypnotizes men. She uses the shell to seize control of Cobra and capture most of the Joes. One of the Crimson Twins aids Scarlett, Lady Jaye, and Cover Girl in rescuing their companions.
Cobra decides to test a new earthquake-causing weapon to disrupt a Japan peace conference. It is up to Quick Kick, Bazooka, and their trainees to stop Cobra.
Cobra kidnaps relatives of the Joe team and uses mind-control technology to turn the Joes' families against them. Their goal is to steal highly unstable explosive crystals.
Cobra unleashes an enormous mechanical sea-serpent that devours any seacraft it comes across, enslaves its captives and grows biggers the more it eats.
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 mission to rescue an archeologist from Cobra's clutches leads the Joes on a strange supernatural journey through the tunnel of an ancient Pharaoh's tomb to a confrontation with Osiris, the Egyptain god of the dead.
Cobra manages to breed dinosaurs with stolen DNA specimens from recently discovered dinosaur fossils. With the new reptilian help, Cobra plans to terrorize civilation.
When Flint goes to visit relatives in a small community by the sea, he learns that Cobra forces have set up the town as a mind-controlling base. By night, Cobra controls the residents and the citizens become an army of slave laborers, forced to construct a secret underwater base.
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?
Dusty's mother has become very sick, and Duke orders Dusty to go home. When Dusty finds out his mother is having financial problems he turns to Tomax and Xamot for money, even if it means giving out G.I. Joe classified information!
G.I.Joe finds out Dusty is the traitor giving out classified information, and they order him to go to jail! Cobra springs him out, but what will happen when Dusty can sense the G.I. Joe's every move, and steals top secret chemicals to destroy G.I. Joe once and for all?!
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.
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.
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?
Cobra stakes out a rock concert & uses a rock group to put subliminal messages into the minds of the audience. When the Joe team breaks up their plans, they even get into the act by performing their theme song as ""The Average Joe Band"".
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!
Lady J receives a strange message from England, informing her she is the heir to an ancient manor. When she arrives, she finds herself thrust into a sinister mystery involving a strange hooded cult, secret passages, and the truth behind Destro's silver mask.
Cobra drugs Shipwreck to make him think he is in his hometown of Springfield, 6 years in the future. Cobra is vanquished forever, G.I.Joe is disbanded, he is married to his lost sweetheart, Mara (who is cured of her aquatic transformatin) and they have a daghter.
Shipwreck discovers that he is really in a facsimile of Springfield on the island of Temple Alpha during the present and finds out that it's people are really synthoids.
