The Shadow Strays Storyline:

Codename 13, a 17-year-old trained assassin is under suspension because of a sloppy mission in Japan. The girl built a conscience when she met Monji, an 11 year old boy who lost his mother to a crime syndicate. When Monji is captured, 13 is hellbent on setting a path of destruction to rescue the boy, including going against her mentor and the organization who hires her, the Shadow.