The movie begins with the G.I. Joe unit, where Duke has been made the leader of the unit. But Zartan, declares all the Joes as traitors, Zartan is impersonating the president of the U.S. The entire Joe unit is attacked in a military strike which lands almost all of them into casualty including Duke. The only people who survive the military air strike are Roadblock, Lady Jaye and Flint.
During this incident, Commander of Cobra is rescued by Shadow and Firefly from the underground prison. Despite of so much security and protection underground, they succeed to rescue the Cobra commander. The three members of Joe unit return to the U.S to rundown gym where they set up the base operation. They learn that Zartan is going to replace the Joe unit with the Cobras. They are shocked by this decision and turn up to their original leader General Colton.