Apocalypse — Joseph Rhea

If you asked the people of Civica what they fear more than the Novum; the mythical ship-eating creature that roams the black water beyond their colony's protective borders, they will tell you it is the Betas; a race of artificial humans created by their ancestors long ago and cast out after the destruction of Earth, the so-called Fall of Man. Now, in the midst of a bloody civil war, those same people have no idea what new danger is fast approaching their colony, and why the return of a small and unassuming cargo submarine called the Rogue Wave will either help trigger humanity's final apocalypse, or be the key to its future survival under the sea. Apocalypse is the final book in the 5-book Novum series, which is also available in one massive (>600 page) volume called "Novum Chronicles"