The Jo's storm COBRA Castle! Cobra hits the GIJoe team on two fronts—at the North Pole and in the Amazon! The Joes fight off hordes of new-style BATs and deploy some new hardware of their own. The Amazon supply depot is destroyed and Duke is nearly killed by Destro’s arctic trap! Duke decides that it’s time for a change in tactics. If COBRA is to be defeated, the team has to go “off the grid”.

After hacking into the Sigma 6 computer and infecting it with a virus, COBRA sends the Dreadnocks on a rescue mission to free their leader, Cobra Commander. Meanwhile, Duke visits General Hawk in the hospital, and Hawk's son, Scott Abernathy, draws some unwanted attention after hacking into COBRA's computer in an attempt to perfect an A.I. system he's been working on.

With Cobra Commander back in charge, COBRA launches an all-out assault on the Joe's headquarters. Meanwhile, Scott Abernathy and his robot dog Spud are relentlessly pursued by the sinister android Overlord Vector.

SNAKE EYES vs. STORM SHADOW!! The ninja brothers duel it out as Snake Eyes tries to rescue Scott. The rest of the JO's try to stop COBRA's new plan: COBRA Coast, even after the destruction of their HQ!

COBRA Coast Climax! Duke, Scott, and the other Joe's race the clock! They have 30 minutes to disarm and destroy a plasma canon or COBRA will be victorious! It's Scarlett vs. Baroness, Heavy Duty and Tunnel Rat vs. Destro, and Duke vs. Cobra Commander! Will they stop the doomsday weapon in time?

It's a race between Baroness and the Joes for a stone of power! When the main Joe team gets ito trouble, it's up to Long Range, Spirit, and Snake Eyes to take up the fight!