Destro builds the Mass Device, which is capable of teleporting objects and people from one location to another. In order to send its beam anywhere in the world, Cobra steals a powerful relay satellite, and captures Duke during the attack.

As Duke tries to escape from Cobra Temple, GI Joe constructs its own Mass Device. The two sides race for three rare elements that power the device, with Scarlett leading the Joes to an arctic mine in order to acquire radioactive crystals.

GI Joe and Cobra battle at the sea floor over heavy water needed for the Mass Device, but must join forces against giant tubeworms; Snake Eyes escapes the crystal mine but is lost in the Arctic while suffering radiation poisoning.

As Stalker tries to trick Cobra into thinking GI Joe has surrendered, the rest of the team heads to South America seeking the third Mass Device-powering element, which is only found in a meteorite at the center of a volcano.

Destro overthrows Cobra Commander and tries to force the world to surrender, but Scarlett leads Cobra's slaves in a revolt from inside Cobra Temple while Duke and the rest of the Joes attack from the outside.