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.

Maru and Kiruko return to Tokyo to find a neighborhood crowded with tents. When Maru goes off to a game center, Kiruko is left to gather information for herself, and hears a scary rumor.

Maru and Kiruko are on the hunt for the Immortal Order. On the way, they stay at a hotel run by a girl named Totori. Dumping their bags and searching for safe drinking water, they stumble upon a badly injured man.

Maru and Kiruko find what they believe is the doctor and the Immortal Order. Instead, it is a hostile organization that is strongly opposed to the treatment that the Immortal Order provides.

Maru and Kiruko decide to head to the Ibaraki facility of the Takahara Academy. Since it's on the way, they agree to help Juichi confirm whether his baby is still alive. Arriving at the Walled Town, the situation is very different to what was expected.