In the middle of the desert and under a dark sky, lights are ignited on a stone mesa and a runway is revealed at the top. Cobra Rattlers, Trubble Bubbles, HISS tanks and Ferrets then launch from the fortress to attack the Joes. Breaker, who is snoring while in the communications room, is awakened by the perimeter alert and starts a red alert.

Flint, Lady Jaye and Heavy Metal catch sight of the mesa on a monitor and Lady Jaye wonders how the base was built without the Joes knowing about its construction. Flint decides to adopt a “shoot first and ask questions later” policy and the Joes rush out to intercept Cobra.

AWE Strikers parachute to the ground, land near the mesa and Flint tells the Joes to go ahead and knock on the front door. As Cobra Rattlers approach trio of Skystrikers, Lady Jaye asks Ace if he would like to accompany her into enemy territory. “Blow in my headphones and I’ll follow you anywhere, Lady Jaye,” Ace replies.

Cobra’s weapons are destroyed by the Joes and suddenly the entire Cobra army disappears. A computer voice announces that the computer simulation has ended and a confused Flint drives with Bazooka into the base. Lady Jaye, Flint, and Airborne land on the roof of the base and enter the base as well.

Both groups of Joe teams meet in the control room and Flint demands that they get the Pentagon involved, however, Col. Sharpe appears on a monitor in the room and explains that the Pentagon is already aware of the base since they authorized the construction. The base is known as Watchdog and is the most sophisticated computer in the world. After Col. Sharpe explains that the Cobra army the Joes fought were holograms and Lady Jaye realizes that the base was never encoded as hostile and therefore not recognized by the Joes satellite system, Col. Sharpe straightens his tie and nervously explains that Watchdog is the new commander of the Joe team. Dr. Hammler, the inventor of Watchdog, enters the room and explains that his creation is a powerful and efficient intelligence network that scans the globe “and beyond” for Cobra activity.

Dr. Hammler also adds that the Joes will receive their orders from Watchdog via a communicator, which he pulls from his coat pocket. “We’re supposed to take orders from a pile of silicon chips?” Flint asks Col. Sharpe. Dr. Hammler suggests that the Joes need a demonstration.

Watchdog finds a yacht called the Cerebus in the Indian Ocean and notes that Cobra Commander and Destro are aboard. Breaker tells Flint that there’s no need for a personnel review since Watchdog has dispatched the USS Flagg to intercept. Dragonflies and SHARCs take off and attack.

After the Skystrikers, which are led by Ace, complete their strafing run, the Cerebus sinks into the water. Admiral Ledger congratulates the Joes and tells them to travel back to the USS Flagg since Watchdog has transmitted new orders. Flint radios the Joes’ aircraft carrier and asks if Destro and Cobra Commander were aboard. Shipwreck flies his SHARC back into the water and discovers that the Cerebus has disappeared.