In the near future, weapons master James McCullen (Christopher Eccleston) has created a nanotech-based weapon – nanomites designed to devour metal and other materials, capable of destroying anything from tanks to cities. The nanobots can only be stopped by activating the kill switch. His company M.A.R.S. sells four warheads to NATO, and NATO troops led by American soldiers Duke (Channing Tatum) and Ripcord (Marlon Wayans) are asked to deliver the warheads. Their convoy is ambushed by the Baroness (Sienna Miller), whom Duke recognizes to be his ex-fiancee Ana Lewis. Duke and Ripcord are rescued by Scarlett (Rachel Nichols), Snake Eyes (Ray Park), Breaker (Saïd Taghmaoui), and Heavy Duty (Adewale Akinnuoye-Agbaje). They take the warheads to The Pit, G.I. Joe’s command center in Egypt, and upon arriving, rendezvous with the head of the G.I. Joe Team, General Hawk (Dennis Quaid). Hawk takes command of the warheads and excuses Duke and Ripcord, only to be convinced to let them join his group, after Duke reveals that he knows the Baroness.
McCullen is revealed to be using the same nanotechnology to build an army of soldiers with the aid of the Doctor (Joseph Gordon-Levitt), planning on using the warheads to cause worldwide panic and bring about a new world order. Using a tracking device, McCullen locates the G.I. Joe base and sends Storm Shadow (Byung-Hun Lee) and the Baroness to retrieve the warheads, with assistance from Zartan (Arnold Vosloo).
After a fight, Storm Shadow and the Baroness retrieve the warheads and take them to Baron DeCobray, the Baroness’s husband, for him to weaponize. Making their way to Paris, the Joes pursue the Baroness and Storm Shadow, but are unsuccessful in stopping them from launching one of the missiles. The missile hits the Eiffel Tower and releases the nanomites in it, destroying the tower and some of the surrounding area before Duke manages to hit the kill switch, but in so doing, he is captured and taken to McCullen’s base under the Arctic.