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 bring panic and bring about a new world order. Using a tracking device, McCullen locates the G.I. Joe base and sends Storm Shadow (Lee Byung-hun) and the Baroness to retrieve the warheads with assistance from Zartan (Arnold Vosloo), inflicting casualties on several G.I. Joe soldiers.
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 and use them to destroy the Eiffel Tower to serve as a showing of the warhead's destructive power. Making their way to Paris, the Joes 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.