The story takes place in the year 2013 after a great conflict in which the planet was devastated, after this military weapons was outlawed and the command given to an independent authority in the 6 remaining regions. The story takes place in one of these regions, the city No.6. Zion, a young boy, was tried at the age of twelve years as a being with an extremely high intelligence and allowed him to live in a luxurious area called "Cronos".
During his twelfth birthday, he meets a charming boy named Nezumi having escaped from a correctional home. Shion protects him, but it disappears the next day without a trace. Zion is deprived of much of its privileges for complicity leak is found and deported to "Lost Town".