The story begins in the perfect city #6 in 2013. When Sion was two years old, he was classified among people with "highest intellect" and allowed to live in the elite district Kronos. On his twelfth birthday, Sion meets a boy named Nizumi (Rat), who had escaped from confinement. Sion helped him, but in return the Public Security Bureau stripped Sion of all privileges and expelled him from Kronos to the "Lost City." Four years after the exile, a mysterious incident leads Sion to the secret of city #6.