While living in the idyllic No. 6, Sion has a fateful encounter with the wanted fugitive, Nezumi.

Four years have passed since Sion's encounter with Nezumi. After losing his special privileges, including the right to live in Chronos, Sion now lives in Lost Town with his mother. One day while Sion is working as a supervisor at a park, he discovers a strange dead body.

Sion gives up everything he has to escape No. 6 with Nezumi. They manage to arrive safely at Rat's home, but it isn't long before a black blister on Sion's neck is discovered.

Karan receives the news of her son being alive and sends a bizarre response. Sion and Nezumi visit a lewd former columnist to understand the meaning of this message.

Rikiga comes with news that another person has aged and died in No. 6 . Safu visits a museum in No. 5. Nezumi suddenly faints on stage.

Safu returns to No. 6 after her grandmother's death and finds out about Sion. Meanwhile, Nezumi disagrees with Sion's goals.

Nezumi secretly proposes a dangerous job to Inukashi. Karan copes with Safu's arrest.

In order to save Safu, Sion and Rat head to the edges of the Western District. There, they meet a legless old man who leads a large group of men. The old man, the person who named Rat, is actually one of the researchers with the young Karan in Rikiga's picture. The man tells Sion that Rat is the last survivor of the forest folk who were wiped out by No. 6, and he also tells them about Elyurias, the reason No. 6 destroyed the forest folk.

With Rikiga's help, Sion and Rat are able to extract information on the correctional facility from a top No. 6 official. They learn that it will be more difficult than they expected to infiltrate the facility. They also learn that No. 6 will engage in a cleaning operation before the Holy Day. On the eve of the Holy day, Sion and Rat are visiting a market in the West District when they encounter the military and find themselves caught up in a large-scale massacre and kidnapping.

Sion and Rat have overcome many difficulties to reach Safu. But once they learn that Safu has merged with Elyurias, Sion becomes enraged. Meanwhile, the people gathered to celebrate the Holy Day have been attacked by a large number of parasite bees. Will No. 6 survive? And what will be the fate of Sion and Rat?