The Mutation (Animorphs #36)

Two of the free Hork-Bajir living on Earth have brought the Animorphs and Ax a terrifying discovery: Visser Three has tried---unsuccessfully---to create a race of amphibious Hork-Bajir.

It seems Visser Three has become fixated on the sunken Pemalite ship he glimpsed and lost (book #27). So, he has arranged the construction of a fabulous new underwater Yeerk craft he calls "SeaBlade," that will be able to locate the Pemalite ship along with it's advance technology. The Animorphs and Ax know they can't let the Visser find the ship. So, after they acquire orca morphs it's a battle between the SeaBlade and six killer whales.

But after damaging the SeaBlade, the kids and Visser Three make a startling discovery: an underwater civilization, a sort of real-life Atlantis populated by mutated humans (gills and lungs) who call themselves Nartecs and live in huge underwater caverns filled with air. The Nartecs seize sunken vessels from the oceans of the world, adapt the ships' technology, and mummify the crews.

So now, the Animorphs and Ax need to survive the encounter with the Nartec and still completely destroy the SeaBlade (whose technology would allow the Nartec to crate havoc in the world's oceans). And in order to do this and escape the Animorphs and Ax will Actually have to fight alongside Visser Three...