Two soldiers stationed in Kazahkstan (Captain Duke Hauser and his partner only going by the name "Ripcord") were ordered to transport a special weapon created by the weapon corporation named "MARS" led by a man named McCullen. But they were attacked by a force led by Anastasia DeCobray (who that Duke has history with), but were saved by a top secret special forces unit only known as "G.I. Joe". The leader of G.I. Joe, General Abernathy (or Hawk) is on the trail of an evil organization known as "Cobra". Duke and Ripcord want to join the Joes to help them defeat Ana and Cobra. Meanwhile, McCullen is secretly working for Cobra and supplying the organization with the advanced weapons of his corporation, one of them includes the "Nanomite" warhead, that once activated can eat any metallic products. As Duke and Ripcord trace Ana to Paris where she plans on destroying the city and to test this new, dangerous weapon. Now, Duke must stop Ana and Cobra before they take over the world, and to prove that he is a Real American Hero.