Four years have passed since Shion's encounter with Nezumi. After losing his special privileges, Sion now lives in Lost Town with his mother. One day at his park supervisor job, Shion discovers a strange dead body.

Shion gives up everything he has to escape No. 6 with Nezumi but, just when they think they're safe, another misfortune befalls Shion.

Karan receives the news of her son being alive and sends a bizarre response. Shion and Nezumi visit a lewd former columnist to understand the meaning of Shion's mother's 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 Shion. Meanwhile, Nezumi and Shion have a disagreement.

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

In order to save Safu, Shion and Nezumi head to the edges of the Western District to meet up with an old acquaintance from Nezumi's past.

With Rikiga's help, Shion and Nezumi are able to extract information about the correctional facility, learning that infiltration will be more difficult than they expected. As Holy Day approaches, they struggle to devise a plan. Yoming reveals his plans for the future to Karan. Safu encounters an unexpected powerful entity that helps her gain consciousness.

The plan to rescue Safu is going as expected but, as Shion and Nezumi get deeper into the facility, Shion’s attitude changes dramatically.

Shion and Nezumi have overcome many difficulties to reach Safu, but the Safu that they find is not what they expected. Meanwhile, those gathered to celebrate the Holy Day are attacked by parasitic bees. Will No. 6 survive and what will be the fate of Shion and Nezumi?