Rise of Cobra: Weapons expert James McCullen has created a nanotechnology-based weapon capable of destroying an entire city. His company MARS sells four warheads to NATO, and the U.S. Army is tasked with delivering the warheads. Duke and Ripcord are delivering the warheads when they are ambushed by the Baroness. The two are rescued by Scarlett, Snake Eyes and Heavy Duty. They take the warheads to the G.I. Joe's command center, rendezvousing with General Hawk. McCullen is revealed to be using the same nanotechnology to build an army of soldiers with the aid of the Doctor.

Retaliation: An elite military unit, comprised of special operatives known as G.I. Joe, has been set up to take the fall for a terrible crime they didn't commit. Now, Roadblock, Duke, and the others must once again face their mortal enemry, COBRA, as well as dangerous new threats operating within the government. When all else fails, one option remains: Retaliation.