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...

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.

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.

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.

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 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.

When Destro discovers a synthoid of himself, he aids the Joes in defeating Cobra's synthoid plot.

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.

Movie producer wants the real G.I. Joes to star in his movie about them after finding actors to be too unrealistic.

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.

Cobra creates a machine that destroys all the money in the country leaving all its citizens vitually penniless.