It's Ninjas vs Cowboys. What's not to like?
People overthink this film.
Ninja reaches his life's ambition and realizes there's nothing else. Killing the baby would render the rest of his life pointless. Also, killing babies is horrible. Saves the baby, turns his back on everything he knows - and goes to create a new one. Learns peace though community, but is ultimately forced to take up the sword. Against oowboys who really, really deserve it. Awesome battle of cowboys vs ninjas starts, and our hero emerges bloody and forlorn. There's no place for him in the world, so he wanders - wanders to keep those he loves safe.
Straight, simple, direct, and awesome.
What more do you really need out of a film? I mean, honestly.