According to an ancient book, Walden finds out that there's an underwater city called "Wuzzlantis". It's residents along with King Triton and the whole city were turned into stone by a Snappity-Snap fish. With the help of Widget's Super Submarine 3000, Wubbzy wishes to go to and save the forgotten city of Wuzzlantis.
When Wubbzy takes out the big Snappity-Snap fish, he was revealed to be a little green fish. After he finishes it off, Wuzzlantis, King Triton and all the city's residents turn back to normal.
The player must navigate Wubbzy through the water with the Super Submarine 3000. He must also avoid baddies and collect shells scattered around the sea for bonus points. They can be retrieved by simply running into them or by blowing bubbles at enemies. They can also be found in treasure chests seen throughout the game. But if Wubbzy touches the enemies or their projectiles, he will lose shells. In stage two, he might find rare golden fish which give lots of shells when collected.
There are three stages: the Kooky Koral Reefs, Cave of the Crunchy Crabs, and Wuzzlantis. Wubbzy must obstacle through the courses and confront baddies including jellyfish, sea urchins, purple fish, crunchy crabs, skeleton fish, and the Snappity-Snap fish at the end. There are also corals, resembling purple kickety-kick balls; whirlpools, rushing waters, and boulders which can be broken by dashing into them. To defeat the Snappity-Snap fish, shoot bubbles at its claws when they pop out and run into them.
The rare golden fish's design was recycled from one of the fishes seen in A Tale of Tails.