The story is set in No. 6, a future model city in 2013. Raised as a top-ranking elite since the age of 2, a boy named Shion lives in an exclusive area in No. 6. On the night of his 12th birthday, he rescues a boy who calls himself Nezumi (Rat). Nezumi ran away from the city's Special Security Area. From that moment on, Shion's life is changed forever...