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.

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.

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.

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.

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.