The game starts with a mysterious Diver out in the middle of the ocean. After searching and swimming around for a little while, the Diver manages to recover and restore two drones that help her navigate through the ocean.

Throughout ABZU a great white shark swims around terrorizing the Diver’s drones, and disrupting the Diver’s deep sea adventures. Along the way the Diver activates portals that frees fish, sending them back out into the vast ocean while also uncovering a secret coven that further restores the marine life every time it’s activated.

Each interaction with the coven also leads the Diver closer and closer to a dark secret buried at the bottom of the sea.

After the great white shark destroys the Diver’s drone guides, the Diver is left to use crude signal communications with the fish to swim alongside them or travel in their packs.

While traveling through some of the darker areas of the ocean, the Diver comes across an area filled with triangular, electric mines. Getting too close sends a shock through whoever touches them. Further into the game the Diver then comes across the great white shark, buried underneath one of the machines that has a similar design to the electric triangle mines.

After freeing the shark from the debris, both the Diver and the shark team up to further explore where the electric mines are coming from. They end up swimming through maintenance tunnels and high-tech corridors that eventually leads to a giant room filled with electric mines, and at the center is a triangular mother brain. The great white shark attempts to attack the brain but the mother brain strikes back, electrocuting both the diver and the shark.

The electrocution is so severe that it destroys the Diver’s outer shell and reveals that the Diver is actually an android. The Diver also discover that the great white shark has died from the electrocution.

Venturing further through the ocean reveals additional portals that frees more fish and eventually the Diver comes upon a giant, secret marina that leads toward a restoration portal that not only feeds more life back into the ocean after it’s activated, but it also restores the Diver’s body and brings back a spirit version of the great white shark.

Riding on the great white shark, the Diver and the shark continue to restore the ocean while destroying anchored mechanical stations that were built by the triangle mother brain. Eventually the shark and the Diver find the massive, sunken space ship that houses the triangle mother brain and they enter into it, blowing up all of the security mines and blasting through the mother brain, destroying it.

Plant life begins to grow around the destroyed ship, indicating that life will continue to flourish while the Diver finds a new home in the ocean.

The Diver was originally one of the underwater scouts from the triangular spaceship, but during the crash the Diver appeared to become separated from the rest of the ship. The drone scouts were attempting to help lead the Diver back to the mother ship, but the great white shark destroyed them, since the mother ship was draining the sea life and attempting to capture certain fish with the portals.

Since the Diver lost her memory and had to go on a journey to rediscover her origins, her priorities change after discovering the beauty of the ocean, and instead of working with the Illuminati space droids, the Diver begins to help free the fish, restore the marine life and eventually team up with the shark to destroy the mother brain.