The Gastrea attack has put humanity in danger of going extinct in the near future. They reside in little neighborhoods dispersed around Japan, where desperation and violence coexist.
Together with his buddies, Rentarou, a second-grader at Magata High School and a member of the Civil Security, battles the threat that is currently present. They are informed by a covert government mission one day that their hometown Tokyo is soon to be destroyed. It is now the responsibility of Civil Security to prevent these plans.