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.

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.

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

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.

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.

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

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.

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.