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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Lady Jaye disguises herself as the Baroness in order to learn about a Cobra weapon created to form whirlpools and tidal waves.

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...

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.

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...