Underneath the water is a Black Pyramid. Megatron has figured out that it is really a Matrix chamber that can amplify the power of Transformers. However, the chamber needs energy to activate, so Slapper and Gas Skunk begin draining power from the powerlines in the water to activate it.

Meanwhile, Koji and Doctor Okase are on a ship to test out its new capability. Koji wonders how they can use it to explore underwater when it's not a submarine. Doctor Okase explains that the ship is capable of a maneuver that no other ship can accomplish, assuming no one else is in the water around the ship at the time.

The Predacons are in the water however, and they fear this will draw the Autobots to them. Sky Byte and Dark Scream move out to destroy it.

Meanwhile, Koji and the doctor prepare to use the ship's exploration capability. The entire ship suddenly changes to a vertical orientation, allowing the observation unit to move down into the water. Koji is eager to see the Black Pyramid. However, when the fish suddenly all begin swimming away, he knows something is wrong. When Sky Byte appears, he crashes into the ship, knocking out several systems. The doctor tries to bring the unit back up, but Sky Byte strikes again, and the doctor is knocked unconscious. Koji quickly radios Optimus Prime to come to the rescue.

Optimus Prime speeds off (from getting washed) and orders Tai to look into that area. She tells Prime about the Black Pyramid and the power lines. Tai activates the Global Space Bridge, calling the Autobot brothers to join Prime. Unfortunately, the Space Bridge only stretches so far. Side Burn offers to try to jump to the ship. He revs up, build up speed and then stops at the last second, afraid of not making it. Prowl goes next, using his boosters to propel him most of the way.

X-Brawn hops into the water in vehicle mode, with Side Burn in tow. Optimus has Tai adjust the angle of the Space Bridge, and then he charges off the bridge in vehicle mode. He transforms into robot mode, detaching from his trailer. Using a fire hose, the propels the trailer forward, using the momentum to pull him onto the ship. As he approaches the ship, he kicks Dark Scream away, sending him into the ocean. Sky Byte suddenly appears and takes on Prime. When Prime criticizes his poetry, Sky Byte attacks! The two grapple and then crash into the sea. Sky Byte goes to shark mode and launches two missiles at the observation unit. Prime counters them, but he is having trouble moving in the water.

Megatron sees all this and orders Gas Skunk and Slapper to help Sky Byte. The two want to, but are being attacked by Autobots themselves.

Tai gives X-Brawn instructions on how to repair the damaged ship. He goes underwater to help as Side Burn goes to help Optimus. Meanwhile, Optimus is letting Sky Byte win the fight to distract him and allow time for repairs. However, once he is down, Sky Byte goes after the ship again. Koji tells Optimus to fight back and the two go at it again. Sky Byte has the advantage however. They are fighting on his turf and he manages to hurt Optimus further. The Autobot leader continues to fight back however.

At the ship, X-Brawn has completed his repairs, and Prowl makes it onto the scene in time to knock the ship back into a horizontal orientation. As the ship rises, it takes Optimus and Sky Byte with it. Sky Byte transforms and threatens Optimus with yet another poem, but this time Optimus is ready and uses his Fist of Steel to knock him into the water.

The battle is lost, and Megatron orders the Black Pyramid destroyed so the Autobots cannot utilize its power.

Back on the ship, the Autobots gather as Koji asks again whether they will ever find his father. Optimus promises they will, just as they are called off to fight the Predacons once again!