Visser Three is still trying to find a way to reach the Pemalite ship that was hidden thousands of feet below the oceans surface. The ship contains technology so advanced that its 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 Earths invasion.

Jake and the other Animorphs acquire additional deep-sea morphs in order to stop the Vissers 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?