Cobra hits the G.I. Joe team on two fronts: the North Pole and in the Amazon. The Joes fight off hordes of new-style B.A.T.s and deploy some new hardware of their own.

After hacking into the Sigma 6 computer and infecting it with a virus, Destro sends Zartan and the Dreadnoks on a rescue mission to free their leader Cobra Commander. Meanwhile, Duke visits General Hawk in the hospital.

With Cobra Commander back in charge of Cobra Command, he launches a full-scale assault on G.I. Joe Headquarters. Meanwhile, Scott Abernathy and Spud are pursued by Overkill's B.A.T. creation Overlord Vector.

While fighting Storm Shadow, Snake Eyes tries to save Scott Abernathy and Spud. Following the destruction of G.I. Joe Headquarters, the other Joes try to stop COBRA's new plan called Cobra Coast.

Duke, Scott and the Joe team find themselves in a race against time as they try to disarm a plasma cannon planted by the Cobra team.

The Joe team goes after a stone of power sought by the Baroness.