When a COBRA spy steals a powerful new technology, the GI JOE team fights back with spies of their own! Duke, Shipwreck, Wild Bill and the rest of the GI JOE team have to strike quickly, before Cobra Commander and his forces turn the stolen device into a dangerous weapon for evil!

After yet another defeat inflicted by G.I. Joe, the immediate subordinates of Cobra's leader, Cobra Commander, have finally come to the end of their patience with his apparent incompetence and his inability to achieve real victories. The leader of the research and interrogations wing, Dr. Mindbender, receives a dream showing the solution. His plan is to collect the genetic material of great warriors and military leaders to create a composite clone that would be the perfect leader for Cobra. Now they set out to put this scheme into motion, and G.I. Joe has very little time to learn of this plot before Cobra becomes that much more a dire threat to the world.