Destro shows the location of Cobra’s launch base to the Joes and adds that one of the Joes is a synthoid. As soon as Cobra Commander learns that Joes have escaped from General Franks, he orders a Tele-Viper to place the Cobra base on yellow alert. Duke and Mutt race inside, use the dock as a ramp and crash into a stack of crates before attacking a couple of Cobra agents and splitting up so they can find the Pentagon’s top brass.

Duke urges the Joes not to listen to Destro’s warnings because Destro wants to create dissension among the Joes. Destro replies that the welfare of the Joes is of no consequence to him since all he wants is for Zartan to learn the hard lesson of angering him, and Destro asks the Joes to leave since their planes are ready and he grows weary of their company.

Admiral Ledger, Colonel Sharp, General Howe and General Franks sit in cell 15 and wonder how they were captured. Their guard tells them to be quiet but he is knocked out by Mutt who winces in pain after hitting the guard from behind. Mutt asks Junkyard if the men in the cell are real people and after hearing an affirmative ‘woof’ from Junkyard, Mutt blows the lock off the cell with a gun.

Dozens of Skystrikers converge on Cobra’s base and Cobra Commander orders the Joes to be destroyed. Laser cannons knock several of the planes out of the sky, but the Joes parachute to safety and continue to attack the base. Scarlett and Duke’s plane is damaged and Scarlett tells Duke that her controls are stuck and that he should save himself. Duke ejects, lands on the ground and watches the plane crash into a cannon. “So much for Scarlett,” he tells himself.

Unbeknownst to the synthoid, Scarlett parachutes to safety and follows Duke to a hidden entrance into the base. Duke attacks her, however, she tosses him around until he has her at gunpoint with her own gun. The real Duke runs into the room and tackles the synthoid of himself to the ground and the two begin to exchange punches.

Scarlett grabs her gun and orders both of them to stop. Mutt, Junkyard and the Pentagon staff enter the room and Scarlett orders Junkyard to attack. The synthoid Duke bolts and escapes through a door that Junkyard bumps his head into and falls to the ground.

Practically draped over his shoulder, Scarlett tells Duke that she is glad to see him in one piece. Outside the base, Ace and the others decide to use their missiles to destroy the cannons while inside Cobra Commander meets the synthoid Duke and decides to eliminate him for his failure, however, the neutralizer is set at the highest setting so all of the synthoids are destroyed.

Cobra Commander and Zartan flee and Duke chases them after ordering the others to destroy the cannons by shooting the control panel. Zartan and Cobra Commander escape the island on a Firebat and nearly fry Duke with the engine’s blast.

In front of the entire Joe team, the real General Franks announces that the Joe team is once again operational and given the highest military honors. And when the speech is over, all of the Joes stand up, raise their fists in the air and proudly shout together: “YO JOE!”