Tenchu 2: Birth of the Stealth Assassins (2000)

Once again, you can play as Ayame or Rikimaru, two faithful and honorable ninja whose lord is a gentle man in an age of warfare. With your training nearly complete, you find yourself caught up in aiding your lord against a civil war in his own domain. All is not what it seems, however, and you'll soon realize that your greatest threat has been forged much like you.