Cobra Commander somehow survived the last time he fought the G.I. Joe team and this time he is plotting to use the long lost powers of the Atlanteans in his bid to rule the world. The game's format is similar to that of Capcom's Bionic Commando series with an overhead map of the various sub-stages, and bosses (Overkill, Cesspool, Firefly, Major Bludd, Destro) located at Cobra bases sprinkled throughout the game. Cobra Commander is the final boss at the end of the game once again.
