Lady Jaye subdues her opponent and before Flint’s adversary can shoot him, Lady Jaye throws a helmet at the Cobra. The Joes don the pilots' costumes and climb insides a Rattler designated as Golden Skull One. The Joes are told by a Cobra radio operator that they are to join their squadron and lead them to Undersea Base Delta, Cobra’s base of operations for the Vortex Cone. “Uh, yeah, right, sure,” Flint tells the operator. “Nothing is going right today,” complains Lady Jaye.

Flint leads the Rattler squadron aimlessly and one of the Cobra pilots asks if he knows where the base is located. Suggesting Lady Jaye tighten her seat belt, Flint flies behind the Cobra Rattlers and destroys three of the six planes, but the remaining three Rattlers fire their missiles the Joes.

Flint streaks into a thick cloud bank and avoids the missiles before firing three of his own at the Rattlers. With the last three Cobra planes destroyed, Flint tells Lady Jaye that their next stop is Joe headquarters.

Lady Jaye drops a heavily warped floppy on a table and Mainframe asks how they could be so cruel to a poor disk. Lady Jaye then leans over, point a thumb at herself and tells Mainframe, “That’s nothing! You should see what Cobra did to me!” Hawk asks if Mainframe could simply iron the disk out, but Mainframe replies that even if he were to starch the disk, he wouldn’t be able to get any information. Duke orders the Joes’ computer expert to do something because time is running out.

While flying his Rattler, Wild Weasel reports that he has found a battleship, three cruisers and six destroyers. Destro orders Wild Weasel to return to base and Deep Six and Wet-Suit follow him in a SHARC. After a giant Cobra head emerges from under the ocean, Cobra Commander leads dozens of Firebats in an attack against the ships, Wild Weasel lands inside the Cobra’s head and the Joes activate a homing signal.

Aboard a transport plane, Flint helps Lady Jaye with her underwater breathing gear and explains that the Joe team will create a diversion so that Deep Six and Wet-Suit can deactivate the Vortex Cone. Lady Jaye asks about the robots on the plane and Flint informs her that if they can stop the Vortex Cone, then they will wreck it with brute force.

The Joes parachute into the ocean, and after Cobra’s alarms are activated, Destro activates the base’s defenses, an army of BATs. Cobra Commander and the Firebats attack the ships spotted by Wild Weasel, but the ships do not fight back. Suspicious of such an easy victory, Cobra Commander examines the remains of the ship and realizes that the cruisers, the battleship and the destroyers were plywood fakes.

While Cobra Commander leads the Firebats back to Undersea Base Delta, the Joes attack, however, they are pushed back by the BATs. The Baroness catches sight of Flint and Lady Jaye on a monitor and exclaims that they are supposed to be dead. But Destro places an arm on her shoulder and tells her that he is glad that they are alive since he can present them as toys to her, and the Baroness rubs Destro’s hand.

While Flint orders the Joes to gut their own robots so they can use them like Trojan horses, Destro orders the BATs to capture the Joe leaders and to kill the rest of the Joes. Lady Jaye is caught by one of the BATs and Flint swims to her rescue, but their oxygen supply is cut off and the rest of the BATs continue to attack the Joes.

Flint and Lady Jaye are dumped onto the floor at feet of Destro and the Baroness, and Destro tells her that she can have anything her heart desires. The Baroness purrs at the uniqueness of his gift, “the last survivors of America’s elite force.” The Joes awaken and cough as air fills their lungs while Destro and the Baroness laugh at them.

Outside the base, Wet-Suit swims past a security guard, who is reading an issue of Cobra Life magazine, and examines the innards of the Vortex Cone.