In the game, Poseidon the Sea God plains to take the magic away from SeaWorld Adventure Park, he hires all his evil servants to help him with his evil plain. Haracio, a friendly Manatee who used to live in Atlantis escapes from Poseidon and enters SeaWorld where he meets Shamu. Haracio decides to have Shamu's help to stop Poseidon with his evil plain, using special abilities called, animal behaviors, Shamu manages to defeat Poseidon and save SeaWorld from it's magic being taken away.
Poseidon's goal was to float his city of Atlantis to the surface and replace SeaWorld with it. He first uses three floating cells to float the city upwards, but Shamu managed to destroy them causing the city to sink back downwards. But then Poseidon had a backup plain, he decides to use the evil Kracken to raise the city, by attaching his tentacles to it and draging it upwards, luckily Shamu manages to use his tail fluke smash to whack the weakest part of the Kracken's tentacles causing the Kracken to let go of the city dropping it. After a wild chase though the city by the Kracken, the Kracken hits the sign in the city center, angering Poseidon, he approaches Shamu and tries to destroy him. A challenging battle begins.
After a long battle, Shamu manages defeat Poseidon and save SeaWorld from disaster. As Poseidon is defeated, he disappears in a blue light beam as he dies.
When Poseidon dies as Shamu defeats him, it's kind of the same way when Ursula dies when Prince Eric defeats her, by sailing a broken up ship right into her.