In the midst of an unstable political climate, weapons developer McCullen has created nanomites— programmable micro-robots designed to devastate entire cities. Under the guise of enhancing NATO's arsenal, he sells four warheads armed with the nanomites to the U.S. government, escorted by an elite military unit led by Duke and Ripcord. However, their convoy is ambushed by a highly skilled enemy mercenary group known as the Cobra, intent on stealing the weapons. The attack is thwarted by the sudden intervention of a top-secret multinational special forces team called the G.I. Joe. Seeing the potential in Duke and Ripcord's expertise and courage, General Hawk, the leader of G.I. Joe, recruits them into the ranks to help secure the dangerous technology.

Duke and Ripcord, now part of the G.I. Joe team, undergo intensive training at The Pit, the team's underground headquarters. Alongside seasoned team members like Snake Eyes, a silent ninja, and Scarlett, a weapons expert, they quickly learn about the sophisticated gear and advanced technology the Joes utilize to combat global threats. As their training concludes, the team discovers that Cobra's plans for the nanomite warheads are far more sinister than simply stealing them for profit. A race against time ensues to locate and safeguard the warheads, leading the team across the globe to prevent catastrophic destruction.