The United States was greatly divided during the Vietnam War. During this time, a young man sees his chance. Ten years after the war's ending, the paramilitary organization known as 'Cobra' seizes control of the government, having covertly established strongholds in every part of the country. The Cobra Commander now controls much of the Americas, having forged a strong alliance with the USSR. The remaining US patriots seek a way to reclaim their home.
In 1982, Dr. Mindbender discovered an alien craft buried in a dormant volcano in Oregon. Finding an amazing species of giant robot inside, Mindbender removed and repaired them, removing their cores for study and installing controls to pilot them directly or remotely as drones. Cobra Commander himself carries a mode-locked Megatron as his personal sidearm, and flies Starscream as his royal transport. With powerful mecha at their disposal, Cobra's army seems unstoppable. However, G.I. Joe have managed to rescue and reactivate a small handful of Autobots and Decepticons, giving them a chance to fight back. Many of the Transformers, awake and otherwise, have been given Cobra vehicle altmodes.
After 50 years of absorbing Earth culture remotely, in 2005 the Junkions launched a ship to search for the broadcast source of the mysterious all-powerful Sponsor. Arriving on Earth, some Junkions joined G.I. Joe in battling the dark forces of Cobra, while others resisted getting involved.
That same year Unicron destroyed Cybertron, and, not finding what the god was looking for, dispatched its agents to scour the cosmos searching for something that is still hidden on Earth. The next planet destroyed and eaten was Junkion, stranding the last of their race on Earth.