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.

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.

Nezumi leads Sion to the edges of the Western District to seek information from a legless old man belonging from No.6's past. Safu finds herself to be a sample of research at the correctional facility.

With Rikiga's help, Sion and Nezumi are able to extract information on the correctional facility from a top No. 6 official. Upon learning that infiltration will be more difficult than they expected, they struggle to devise a plan just as Holy Day comes around. 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 the further Sion and Nezumi go inside the facility, Sion’s attitude changes dramatically.

Sion and Nezumi have overcome many difficulties to reach Safu. However, Safu has now merged with Elyurias. 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 Nezumi?