When 9 first comes to life, he finds himself in a post-apocalyptic world. All humans are gone, and it is only by chance that he discovers a small community of others like him taking refuge from fearsome machines that roam the earth intent on their extinction. Despite being the neophyte of the group, 9 convinces the others that hiding will do them no good.
All life on Earth is extinct. Several robots are built out of animal bones, one of them essentially being an entire cat skeleton, and a protagonist wears a bird skull as a helmet.
Sort of. An antagonist absorbs souls into itself, akin to eating them. Another antagonist has a snakelike, fabric body designed to carry captured victims inside of, but it opens up at the seam rather than her needing to swallow them.