After the G.I. Joes are framed as traitors by Zartan, who is still impersonating the President of the United States, the Cobra Commander now has all the world leaders under Cobra's control, with their advanced warheads aimed at innocent populaces around the world. Outnumbered and out gunned, the Joes form a plan with the original G.I. Joe General Joseph Colton to overthrow the Cobra Commander and his allies Zartan, Storm Shadow and Firefly.