Japan has collapsed after the Great Disaster. Kiruko accepts a request to take a boy named Maru to a place called Heaven. Meanwhile, children live behind the walls of a nursery in luscious green surroundings. After receiving a mysterious message, Tokio begins to doubt the world around him.

Five years ago, in Asakusa, Robin, Haruki and his racer sister Kiriko had spent their days happily living in an orphanage.

Tokio is taken to see some bizarre-looking babies, and realizes just how little he understands about his surroundings. On a boat with no escape, Maru and Kiruko suffer a terrifying attack. As all is failing, it is up to Kiruko to devise a new strategy.

Maru and Kiruko arrive in a prosperous marketplace. It's the town where the rumored Ministry of Reconstruction runs things. Meanwhile, the academy is suddenly under attack. While trying to take shelter, the children find a hole in the wall.