The Joes re-team to prevent Cobra from achieving world domination, following the events of G.I. Joe: The Rise of Cobra. After neutralizing the Nanomite threat and imprisoning Cobra Commander and Destro, the Joes are called upon to secure Pakistan's nuclear warheads. However, they are decimated in a surprise attack, leaving only Roadblock, Lady Jaye, and Flint as survivors. The Joes soon discover that an impostor is pretending to be the president and that Cobra Commander is planning to take over the world using a revolutionary new weapon.

G.I. Joe: Retaliation
G.I. Joe must navigate a treacherous double threat as they battle both their arch-nemesis Cobra and corrupt government forces seeking to dismantle the team.