Cobra Commander threatens to unleash a deadly mind numbing gas on the world unless they surrender to Cobra...

The Cobras escape from Alcatraz and prepare to use their new weapon to take over the world, now GI Joe has to stop their most devious scheme yet...

Duke is captured by Gnawgahyde who uses a device called the Mind Mangler to try and break into Dukes brain, but a girl named Megan helps Duke escape, little does he know that Megan is really a disguised Zarana planning to steal GI Joes secrets...

After a battle, Cobra Commander and Pathfinder become lost in the Jungle with a enraged Gorilla in pursuit...

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...

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...

Cobra Commander, Destro and Metal Head allow themselves to be imprisoned in Alcatraz so that they can gain access to a highly powerful weapon on the Comstock Lode submarine outside of the prison...

Destro creates a super computer named BIOK, which infiltrates every computer system in the world, but soon BIOK turns on them and has plans of its own to take over the world...

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.

The Joes rush to prevent Cobra from planting its huge cubes as Shipwreck and Snake Eyes try to evade detection.

When the Joes seek to recover a sample of anti-matter from a sunken ship, Zarana is sent to their headquarters to sabotage the operation. She and Mainframe discover they have feelings for each other. In the aftermath of a battle, the USS Flagg is sunk.

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.

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 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.

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.

An aging admiral learns that his ship is to be scrapped, and he turns to Cobra for help. Cobra renders his ship impervious to electronic vessels, so G.I. Joe must use the two-hundred-year-old USS Constitution to defeat him.

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.

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!

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.

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.

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.

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.

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.

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.