The Mutation by K. A. Applegate

Visser Three is still trying to find a way to reach the Pemalite ship. The ship that was hidden thousands of feet below the ocean's surface. A ship containing technology so advanced that it is superior to anything even the Andalites have built. And this time, the visser plans to find the ship so he can use the power to complete Earth's invasion.

Jake, the other Animorphs, and Ax acquire additional deep-sea morphs in order to stop the visser's plan. But while trying to destroy the Yeerk ship, the kids make a startling discovery: an underwater civilization. Have the kids discovered Atlantis . . . or is it just another trap?