A Shadow in the Deep — Anthony Pryor

Lost in time, the Shepherd must save a drowned world.

Disaster strands Alex St. John -- the Shepherd, wielder of a goddess's mystic weapon -- in a drowned world conquered by Tulxatash, a sentient ocean known as the Shadow in the Deep. Meanwhile Alex's comrades face the very catastrophe that destroyed the world, and must ally with their greatest enemies to turn back the deluge and save their lost friend.