Duke leads the G.I. Joe Team to North Korea to find a North Korean defector. Later, Zartan, impersonating the President of the United States, frames G.I. Joe for stealing nuclear warheads from Pakistan after the death of its President during a civil war, and subsequently eliminates G.I. Joe, which kills Duke and the other Joes, using a military air strike. Heavy machine gunner Roadblock, rookie sniper Flint, and counterintelligence officer Lady Jaye survive the attack by diving into a well, and they return to the United States and find the original G.I. Joe, General Joseph Colton, who provides them with weapons.
Meanwhile, Storm Shadow, who survived the Arctic base s destruction,[N 1] and demolitions expert Firefly rescue Cobra Commander from an underground maximum-security prison in Germany, leaving Destro behind. Storm Shadow retreats to a temple in the Himalayas to recover after he was injured. The Blind Master, leader of the Arashikage Clan, sends Snake Eyes and his apprentice Jinx, to capture Storm Shadow, allowing him to answer the murder of his uncle, the Hard Master.
After Zartan announces that Cobra will become the premier U.S. special forces team, replacing G.I. Joe, Lady Jaye deduces that someone is impersonating the President and steals a sample of the President s DNA and confirms that he is Zartan. They escape after a confrontation with Firefly and Zandar, the head of the U.S. Secret Service s Presidential Detail and a member of Cobra. Colton leads the Joes to infiltrate a fundraising event where the President attends it.
Snake Eyes and Jinx locate and capture Storm Shadow after a battle with some ninjas loyal to Storm Shadow and take him back to Japan, where Storm Shadow proclaims that he did not kill the Hard Master and proves it by fighting Snake Eyes with the weapon that killed the Hard Master, which breaks. Knowing that Arashikage steel does not break, the Blind Master deduces that Zartan was the one that murdered the Hard Master and framed Storm Shadow for it, who joined Cobra to bring it down from the inside. With him cleared of murder, Storm Shadow then accompanies Snake Eyes and Jinx as they join the Joes efforts to stop Cobra and avenge the Hard Master.
Zartan invites the world leaders to a summit at historic Fort Sumter, where he blackmails them into disabling their nuclear arsenals, and reveals that he has created Project Zeus: seven orbital kinetic bombardment weapons of mass destruction at his command, destroys Central London to prove his superiority, and threatens to destroy other capitals if the countries do not submit to Cobra. Storm Shadow betrays Cobra Commander and starts a fight, revealing Cobra s deception to the world leaders. Colton kills Zandar and rescues the real President with Lady Jaye, while Storm Shadow kills Zartan. While Snake Eyes, Jinx, and Flint fight Cobra s soldiers, Cobra Commander activates the remaining six weapons and instructs Firefly to protect the launch device, and escapes onto the helicopter. Roadblock and Firefly fight, but Roadblock is able to deactivate and destroy the orbital weapons, as well as kill Firefly. Storm Shadow leaves after avenging his uncle.
At the White House ceremony, the real President addresses the nation and commemorates the Joes, who were awarded by Colton: Roadblock, Jinx, Flint, Snake Eyes, and Lady Jaye. Colton presents Roadblock with an M1911 pistol that belonged to General George S. Patton; to use it to find Cobra Commander. Roadblock proudly raises the weapon and fires a single shot in honor of his fallen comrades, vowing to avenge them.
