Church of Rain by Julian M. Miles

This planet has known many powers. Some have been regarded as divine. Several are departed, but not necessarily gone. These powers have often clashed. Myths tell of cataclysms, atrocities, and stranger events. Roy often dreams of an impossible church. He’s sure it’s waiting for something. That something just happened. It's going to kill him unless he can work out what it is, and how to stop it.