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.

Sion and Rat visit a former reporter for the Latch Bill newspaper to learn the meaning of the message from Karan. Sion is troubled by the savage world outside the city, but eventually, they find Rikiga, the man they are looking for. They learn that Rikiga , who once sought to unravel the mystery of No. 6, now makes his living by selling women to the officials of No. 6.

Safu has returned to No. 6 because of her grandmothers’ death. While back, she learns of what has happened to Sion. At the same time, Sion and Rat continue their discussion over the future of No. 6 and the parasite bees.

Rat learns from Karan's note that Safu was taken by the Bureau of Peace. However, he decides to hide this information from Sion and secretly request that Dogkeeper obtain information on the correctional facility. However, unbeknownst to Rat, Sion and Rikiga are visiting a used clothing store where Sion discovers Safu's coat that was smuggled from the correctional facility. Meanwhile, Safu is being treated as a "sample" by the researchers at the facility where she was taken.

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.

The plan to rescue Safu is going as expected. But the further Sion and Rat go inside the facility, Sion’s attitude changes dramatically.

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?