In 2013, after the great war devastated the world, six city states remain, created by The Babylon Treaty. Sion is a boy assessed as having the highest-ranked intelligence at age 2, allowing him access to the luxurious Cronos living area. On his 12th Birthday, he meets a troublesome boy called Nezumi, who has just escaped from a reformatory and on the run from the authorities. As punishment for harbouring a fugitive, the Public Security Bureau strips Sion of all his privileges, resulting in expulsion from Cronos. After four years of banishment, Sion and Nezumi meet again, resulting in the revelation of the secrets and mystery behind the city No. 6.