Following the events of The Rise of Cobra, Duke (Channing Tatum) has become the leader of the G.I. Joe unit, which is framed for stealing nuclear warheads from Pakistan by Zartan (Arnold Vosloo), who is impersonating the President of the United States (Jonathan Pryce). The unit is subsequently eliminated in a military air strike with Duke as one of the casualties. The only survivors are Roadblock (Dwayne Johnson), Flint (D.J. Cotrona), and Lady Jaye (Adrianne Palicki).

Meanwhile, Storm Shadow (Byung-hun Lee) and Firefly (Ray Stevenson) rescue Cobra Commander (Luke Bracey) from an underground maximum-security prison in Germany, leaving Destro behind. Storm Shadow is injured during the escape and retreats to a temple in the Himalayas to recover. Upon learning that he is alive, the Blind Master (RZA), leader of the Arashikage Clan, sends Snake Eyes (Ray Park) and his apprentice Jinx (

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