The story is set in "No. 6," a future model city in 2013. Raised as a top-ranking elite since the age of two, 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...