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.

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.

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.

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!

The G.I. Joe team gets sent to another dimension in which Cobra took over 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.