Two soldiers stationed in Kazahkstan (Captain Duke Hauser and his partner Ripcord) are ordered to transport special warheads created by MARS, an arms manufacturer controlled by James McCullen.

When they are attacked by thieves (led by Anastasia DeCobray, with whom Duke has history), they are saved by a top secret, international special forces unit known as G.I. Joe. The leader of G.I. Joe, General Abernathy (or Hawk) is on the trail of the thieves: an evil organization called Cobra. While Duke and Ripcord train to join the Joes, McCullen (Destro) is secretly working for Cobra and plotting to recapture his metal eating Nanomite warheads. Duke and Ripcord (with help from Heavy Duty, Snake Eyes, and the rest of the Joes) must prove that they are Real American Heroes by stopping the launch of these warheads before Cobra uses them to take over the world.