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.

At a strange inn, Maru and Kiruko sink into a drowsy slumber. They awaken to something monstrous under the faint light of the moon. At the nursery, Tokio becomes more suspicious of the world around him. Meanwhile, Shiro receives an unexpected message.

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 discover that Dr. Usami had a button with the same pattern as the logo they found on the Kiru-Beam. They decide to follow it's trail, and meet a mysterious informant along the way. Meanwhile, back at the nursery, an emergency meeting is held.

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.