Codename 13, a 17-year-old assassin, finds herself suspended after a botched mission in Japan. During this time, she develops a sense of morality after encountering Monji, an 11-year-old boy whose mother was killed by a criminal syndicate. When Monji is kidnapped, 13 becomes determined to save him, even if it means defying her mentor and the organization that employs her, known as the Shadow.