Weapons expert James McCullen has created a nanotechnology-based weapon capable of destroying an entire city. His company MARS sells four warheads to NATO, and the U.S. Army is tasked with delivering the warheads. Duke and Ripcord are delivering the warheads when they are ambushed by the Baroness. The two are rescued by Scarlett, Snake Eyes and Heavy Duty. They take the warheads to the G.I. Joe's command center, rendezvousing with General Hawk. McCullen is revealed to be using the same nanotechnology to build an army of soldiers with the aid of the Doctor. Storm Shadow and the Baroness use a tracing device to find the weapons and take them to Baron DeCobray for him to weaponize and use them to destroy the Eiffel Tower. The Joe's pursue them through the streets but are unsuccessful in stopping them from launching the missile. Duke manages to hit the kill switch, but in doing so he is captured and taken to McCullen's base under the Arctic. While Scarlett and Snake Eyes attempt to shut down the Arctic base, Duke learns who the Doctor really is.