Bazooka, Alpine and Quick Kick get free and escape on some Trubble Bubbles that were in the back of the cargo jet then commandeer a Cobra chopper.
On Space Station Delta, Junkyard grabs the whistle from around Torch's neck and Mutt blows the whistle turning the Fatal Fluffies back into little harmless creatures. With the Joes controlling Delta, the Pyramid of Darkness is no more.
Shipwreck and Snake Eyes arrive riding cattle to the rebuilt G.I. Joe Headquarters with the disk. Once the power is back on they can read the disk and find out that there is a self-destruction device at Cobra Temple.
Meanwhile, Cobra Commander takes charge again of Cobra and has Destro set up a low altitude pyramid. But it isn't stable, so the Joes have at least some power.
Bazooka, Alpine and Quick Kick's chopper crash lands right in Joe HQ. Since they know where the temple is, the Joes launch a massive assault against the temple. At first they are held back by the Cobra Dragon which immobilizes the Joes with its heat stroke beam. However, Alpine's yodeling shatters the Dragon and the Joes are able to enter the temple and activate the cube's self destruction device. Cobra Commander and the Crimson Twins escape in a jet and are followed by the Joes to the Enterprise Towers, which turn into a giant rocket.
Shipwreck and Snake Eyes meet up with Satin again and together they get into the rocket's command center. Satin magnetizes Cobra Commander's head to the control panel shorting it out. The Joes escape in Trubble Bubbles.
On Delta, Zartan and the Dreadnoks escape. Zartan leaves in the escape pod while the Dreadnoks go out with the trash. Duke and the others rig up a proton beam and blast the Cobra rocket. Cobra Commander and the Twins had already escaped. The Joes celebrate in Enterprise City and the Cobra gang go on to a subway in disguise; Cobra Commander as a woman, Destro a construction worker, Baroness a nurse and the Twins in their usual suits blaming each other.