Shipwreck tells Cutter to use the vertical thrusters and the WHALE rises above the water and the torpedoes fly under the Joes’ hovercraft. The docks are damaged by the torpedoes and the Joes destroy the Moray in their counter-attack. As they shout and congratulate themselves, the WHALE is struck from behind by a Cobra Water Moccasin, which has the Baroness in the gun turret and Major Bludd in the driver’s seat.

But the Water Moccasin is also hit from behind and is destroyed by a Cobra submarine, which avoids the angry Baroness and proceeds toward the Joes. Shipwreck orders the missiles on the hovercraft to be armed, but the hatch on the submarine pops open and Lady Jaye yells to her teammates that she borrowed the sub from Cobra. “YO JOE!” shout the Joes, and they dive underwater and head to Cobra base.

Bazooka parachutes to the television station transmitting the subliminal messages and meets Breaker outside. Realizing that he forgot the darts, Bazooka apologizes.

Shipwreck receives docking instructions and after the Joes climb out of the sub, Lady Jaye orders Tripwire to disarm the missile while the other Joes and herself will rescue the townspeople. They run out and whisper together: “Yo Joe.” Cobra Commander sees the Joes on a monitor and orders the citizens of Pleasant Cove  to defend the city at all costs while on the monitors around the city. The Joes arrive at a crossroads and are surrounded by the townspeople. Lady Jaye tells the Joes not to harm the people. Shoving the people back from them, the Joes try to defend themselves. Flint arrives and tries to choke Tripwire, but Tripwire breaks free and runs off to disarm the missile. Barbecue tells Lady Jaye to follow Flint and try to stop him.

As the Baroness and Zartan argue over who is to blame for the Joes appearing in the city, Cobra Commander screams at them to be silent since he is watching something very interesting: a brain-washed Flint attacking Lady Jaye. While the Joes are inside an airlock, Cobra Commander orders Flint to close the door to the city and open the sea door.

Inside the television station, Bazooka looks at the dart board, which is on television and tells Breaker that he doesn’t understand what is going on. And Breaker hopes that Cobra Commander won’t know either. Tripwire examines the missile’s wiring system and realizes that if he touches the missile it will launch immediately and that he has ten minutes to figure out what to do. Cobra Commander watches the Joes attacked by the citizens and before Flint turns the door’s handle, he grabs his head in pain. The Pleasant Cove townspeople run off to the sub and climb aboard while Lady Jaye hugs a confused Flint and shouts at him, “Flint! You’re back!”

Destro informs Cobra Commander that someone must be interfering with the subliminal transmissions on the television, and while the picture of Cobra Commander from Breaker’s dart board is on the airwaves, Cobra Commander asks, “Who is that fool on TV?” Bazooka removes the dart board from screen and sticks his tongue out at Cobra Commander while Breaker yells, “Ignore Cobra Commander! He’s a jerk!” Enraged beyond measure, Cobra Commander shoots the screen and then turns to face the Joes who enter the room armed and Flint tells Cobra Commander that he is finished. But the rocket launches and Cobra Commander declares himself the victor.

Tripwire runs into room and tells the Joes that he wasn’t able to deactivate the rocket. Cobra Commander insults Tripwire by calling him incompetent and also tells him that the world will now pay the price. However, Tripwire replies, “Not really. I rerouted it. It’s heading straight out to space.” Cobra Commander pushes a button and the Cobra elite descend on a platform and escape while the explosions begin to tear the base apart. As water floods the city, the Joes sprint back to the Cobra submarine and escape. While the Cobra city begins to fall to pieces, Flint tells Cutter, Barbecue, Shipwreck, Polly, Quick Kick and Lady Jaye that even though the sub is small, he loves the speed.

With two AWE Strikers parked in front of his house, Ted asks Flint if he thinks Cobra is gone for good, but Flint tells his cousin that it’s not likely and adds that the only thing that is gone for good is his car and his vacation. Lady Jaye then tells Flint the Colonel Sharpe has offered Flint another two weeks of vacation, and Ted tells Flint that he’d love to have Flint hang out for awhile. But Flint replies, “I want to get back on duty - where I can get some peace and quiet.” And Ted, his wife, Flint and Lady Jaye burst out laughing.