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.

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.

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.