Deep Six finds Duke on his sonar and radios Torpedo that Duke is directly underneath his parachute. Swimming toward the parachute, Torpedo finds Duke, slips a mask over him and grabs him before grasping a railing on the bottom of the SHARC, which escorts them to safety before a shark attacks them. Zartan signals Cobra Commander that the first phase is complete and the synthoids are placed upon a platform on the Cobra sub.

Scarlett radios Shipwreck and asks if he could sink a couple of Cobra Morays for her, and he happily replies, “Does Popeye like Spinach?” As another Moray explodes, the two remaining ships dump canisters into the water which release a smokescreen around the command ship. In the midst of the smoke, the Cobra submarine surfaces and deposits the synthoids in the command ship’s control room via a crane with a flexible and retractable arm that returns to the sub after the sythoids place the top brass on the platform and Zartan climbs on. Meanwhile, Wild Bill destroys the last two hydrofoils.

The submarine dives and both Duke and Scarlett are scolded by General Franks for their inadequate performance against Cobra and orders them to return to the Joes land base. Duke tries to convince Col. Sharp that the Joes should investigate the purposeless attack. However, the request is denied and as Duke and Scarlett walk out, Duke suggests that they not tell the others about the General’s reaction. Scarlett reluctantly agrees.

Cobra Commander explains that the next step in the plan will involve the creation of a Joe team member but first Cobra Commander and Zartan have a surprise for the arms dealer: a synthoid of Destro himself who bows when commanded. Destro demands the destruction of the synthoid and Cobra Commander pulls out a device called the neutralizer and is about to push the destruction button when Zartan rushes forward to stop him. He reminds Cobra Commander that the range of the neutralizer is set to destroy all of the synthoids. Readjusting the range with a lever, the device destroys the synthoid of Destro. Cobra Commander apologizes for almost ending all of the synthoids’ lives and then tells Destro that even Cobra’s weapons dealer can be replaced.

At the next budget meeting, a committee member asks General Howe if he is sure about his recommendation to cut funding for the G.I.Joe program in half. General Franks is asked for his opinion and announces that he agrees with Howe and even believes that they should get rid of the entire team. The committee decides to put the budget changes into effect immediately.

Cover Girl and Clutch fail to replace a tread on an Armadillo due to a lack of parts and Rock ‘n’ Roll finds only a hand full of cartridges available for target practice. As Duke and Scarlett mull over Cobra’s senseless attack, Junkyard rushes up to Duke and begins to lick the First Sergeant after he scratches him on the head. Mutt calls Junkyard back and suddenly Joes are running toward Duke explaining that there’s not enough fuel for one Skystriker and the Joes are running out of oil and gas for the other vehicles. In short, the base is falling apart.

Duke tries to reason with Col. Sharp, however, Duke is told that he should contact General Franks, who is on his way to inspect the base as they speak. As soon as Sharpe signs off, a screen filled with Cobra Rattlers flying toward the Joes’ headquarters appears. Breaker patches Duke into the base intercom system and Duke announces that all airplanes have been grounded so they should prepare for a surface to air attack.