In an ongoing conflict against the nefarious terrorist group Cobra, the elite military unit known as the G.I. Joes has emerged victorious time and time again. But the battle is far from over. After completing a successful mission to secure a nuclear warhead, the team—led by Duke and his second-in-command, Roadblock—is betrayed from within when the President of the United States is impersonated by the sinister Zartan, a master of disguise and member of Cobra. Under the orders of the faux-president, an airstrike is called upon the G.I. Joe unit, obliterating most of the team and leaving only a handful of survivors. The few Joes who escape must now grapple with a world where their government has declared them enemies, and they are forced to operate in the shadows to clear their names and uncover the depth of Cobra’s infiltration.

Driven by a burning need for vengeance and justice, the remaining Joes formulate a plan to fight back. While Roadblock, Lady Jaye, and Flint work to uncover the conspiracy and expose the imposter President, they recruit the original G.I. Joe, General Joseph Colton, for his expertise and leadership. Meanwhile, another Joe, Snake Eyes, pursues his own mission to locate and contain Storm Shadow, an ex-Joe now siding with Cobra. As they navigate a minefield of danger and deceit, the Joes must also contend with Cobra's ultimate plot to assume control of the world through wide-reaching chaos and powerful new weaponry.