Zartan and Cobra seize the Delta Space Station and destroy G.I. Joe headquarters. Shipwreck and Snake Eyes are lost behind enemy lines while Cobra Commander reveals his plan to deprive the world of electricity.
G.I. Joe sets up temporary headquarters on the U.S.S. Flagg. On the Delta Space Station, Dusty, Buzzer and Mutt work to warn the Joe team about Cobra's plan to plant cubes at strategic locations in order to create the pyramid of darkness.
G.I. Joe sends teams to different parts of the world in order to stop Cobra from planting their electronic cubes. Meanwhile, Shipwreck and Snake Eyes continue to lay low behind enemy lines.
Alpine and Bazooka make an ally in Quick Kick. Meanwhile, Tomax and Xamot betray Cobra Commander and take control of Delta Space Station and the Pyramid of Darkness for themselves.
Cobra uses Tomax and Xamot's company Extensive Enterprises to purchase the Red Rocket food chain and use its location as a network of secret missile launching bases. But, the JOE team catches on to the conspiracy.
Cobra tries to steal a spy satellite but Breaker stops them by forcing the satellite to crash in the African jungle. Efforts to recover the satellite by both Cobra and G.I. Joe are complicated by a tribe of African primitives.
In a plan to attack the world's cities with lava, COBRA kidnaps Dr. Shakur and his technology to accomplish this. Can the Joes save the doctor from Cobra's jungle base and destroy the weapon before cities are turned into literal hot spots?
COBRA gains new allies: the animal kingdom, through "High Freq", an animal mind control device. In a race against time, the Joes must stop "High Freq" before Mutt loses the fight against Junkyard, his best friend who is now his worst enemy.
While infiltrating a COBRA temple to save a group of kidnapped scientists, the Joes find the temple filled with funhouse attractions, designed not to amuse, but to stop the Joes in their tracks, permanently.
When Shipwreck tries to show "reporter" Hector Ramirez and his crew that the Joe / Cobra conflict is real, he soon provides all the proof he needs, when COBRA captures them during an operation to steal volatile gas from a weapons arsenal.
When the Joes and COBRA find out that the nitrogen fuel that was stolen from the Joes can also "fuel" the growth of fruits and vegetables, they begin to do battle for the fuel, in a landscape of plants of gigantic proportions.
When the Aurora Borealis begins to go haywire and starts to melt the polar icecap, the Joes and a group of scientists go up north to try to prevent a disaster that could have global implications.
Cobra Commander has a plan to defeat G.I. Joe without firing a shot: replacing the officials that's over the Joes with Synthoids, an artificial life form. But Cobra Commander has placed another Synthoid in a place no one would ever expect.
The Joes have never seen a worse day: disbanded by the government, fugitives from the military, and betrayed by an impostor in their ranks, this truly is the end of G.I. Joe, that is, unless they accept help from a very unlikely source.
Through gypsy magic, Cobra Commander gains 3 new forces in the fight against G.I. Joe: a WW1 pilot, a Mongolian princess, and a Roman centurion, which gives the Joes a new dilemma: How do you stop the enemy when they're not flesh and blood?
The Joes go to Hollywood when hired as technical advisers on 'The G.I. Joe Story', to add realism to the film. But the studio may get more realism they can handle when there is a Firebat at the studio that COBRA wants back, at any cost.
When Robert Harper's rival in the mayoral race keeps sending gang members to reap havoc and ruin Harper's campaign, the Joes are sent in to restore law and order, but Scarlet and Lady Jaye soon find out things are not what they seem.
COBRA invents a machine that can destroy paper money at a distance, and the Joes must get to the bottom of things and destroy the machine before COBRA can flood the world with their own dubious currency.
A COBRA spy has infiltrated the Joes Base, and stole a security code that allowed COBRA to steal a highly advanced laser guidance system. Could the spy be Quick Kick's girlfriend, Amber?
Cobra steals a dangerous bacteria and an experimental growth serum. When the two are accidentally combined, a powerful monster is created that must be stopped by G.I. Joe.
A mysterious person calling himself the Viper is leaving cryptic messages on one of the Joes answering machines. When the Joes investigate the messages, they encounter Cobra. The Joes and Cobra want to find out who is this mysterious Viper and how he knows so much about Cobra.
The Baroness has found the Conch of the Sirens, used by the Sirens to control men, and has used it on the G.I. Joe and COBRA males. Can Scarlet, Lady Jaye, and Cover Girl find a way to break the Baroness's control over the men of G.I. Joe?
In an attempt to stop a world financial summit, COBRA decides to use an artificially created earthquake to get the job done. Can the Joes put a stop to COBRA before COBRA puts a stop to the meeting?
An explosion at a COBRA lab creates a cluster of explosive crystals, a substance that COBRA wants very much, so Cobra Commander kidnaps a group of people that he knows will get the job done, much to the shock of the Joes.
The Joes try to dispose of the highly explosive crystals before COBRA gets their hands on them, while trying to find a way to release their family members from being under the effect of the COBRA brainwashing.
When on an island to repair a Joe vehicle, Bazooka sees a sea serpent, part of Cobra's plan to control the sea lanes, but when the serpent's remote is accidentally destroyed, it soon becomes an out of control, and very ravenous machine.
While the fleeing from the Joes, Storm Shadow finds Arthur's legendary sword, Excalibur. In addition to stopping Cobra's latest scheme, the Joes must also return Excalibur to its resting place.
Some Joes start to have doubts about whether or not the fight with Cobra is doing any real good. Maybe they should just stop fighting. A small group of Joes find themselves in a place where the Joes have apparently lost to Cobra.
Part 2 of 2. Trapped in the alternate Cobra - controlled world, the Joes find an unlikely ally in the Baroness. With her help, Stealer, Clutch and the others search for a way back to their own reality. But Cobra is closing in...
Cobra finds a tablet with a perfume used by Cleopatra. The scent makes men fall for which ever female wears it. The Baroness uses the formula to woo a rich single bachelor. Flint tries to stop her, but he's affected by the perfume as well. It's up to Lady Jay to stop her, she'll get some help from an unexpected ally.
After successfully infiltrating Joe headquarters using very unusual means, COBRA plans on ruining Christmas in Keystone City by attacking the city in Joe vehicles. Can G.I. Joe stop COBRA from spreading their kind of "Christmas Cheer"?
When Lady Jaye decides to help a man get revenge against COBRA for injuring his family, they end up trapped on an island that is being used for the testing of a COBRA weapon that eliminates the power in vehicles.
COBRA has found the temple of Osiris and seeks the treasure within, and the Joes are in hot pursuit. But who will win at the end of the day: The Joes, COBRA, or something else?
Dinosaur bones, a cloning device, and a rapid growth formula all add up to Cobra's new addition to their ranks: living, breathing dinosaurs, a force that even the Joes may not be able to stop.
The good news: Flint goes to Pleasant Cove on vacation to see his relatives on vacation. The bad news: Flint finds out that they, and the whole population of the town are Cobra's brainwashed slaves, and Flint may soon be joining them.
Dusty and Footloose both vie for the attention of a female scientist during their mission: Getting her to the Joes so she can reveal the secrets of Cobra's powerful plasma cannon before COBRA catches them.
While on a Joe mission to locate a downed sub, Shipwreck saves a woman with blue skin named Mara, and soon finds out why she has blue skin: She's what, in old sailor's terms, is called a mermaid, and COBRA wants her back.
Just as the Joes perfect a new body Armour formula, they find evidence to suggest that one of them is giving their secrets away to Cobra. All the evidence seems to point to a senior Joe agent.
Duke's been injured. The traitor has been discovered, now the former Joe is working for Cobra. The Joes must capture their former comrade, but he knows their methods, and can anticipate their moves. The Joes are soon captured, but an unexpected turn will reveal what's really going on.
The Joes get a new weapon to fight COBRA: "WATCHDOG", a computer designed to keep track on Cobra's actions and assign Joes to go stop the threat. But Shipwreck soon finds out what this WATCHDOG is actually programmed to put it's "bite" on.
The COBRA Television Network is on the air, everywhere, on every channel, and the Joes must go into orbit to bring down Cobra's broadcasting satellite before COBRA takes over the world through the world of Television.
While battling COBRA, the Joes gets two visitors: The Oktober Guard (the Russian version of G.I. Joe), and aliens. Now the Joes and The Oktober Guard must join forces to find out who the aliens are, and what their purpose here on Earth is.
