In near future, mankind has been defeated by the viral parasites named "Gastrea." They have been exiled into a small territory and live in despair, side by side with terror. In this world trapped in darkness- Rentaro, a boy living near Tokyo and a member of the "Civil Security" - an organization specializing in fighting against the Gastrea - is used to accomplishing dangerous tasks. His partner is Enju, a precocious young girl. They fight using their peculiar powers until one day, they receive a special assignment from the government. This top secret mission is to prevent the destruction of Tokyo...