Sion's life turns upside down on his 12th birthday when he aids a fugitive named Nezumi. Four years later, their paths cross again as Sion unravels the dark secrets hidden within the utopian city of No. 6.
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.
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.
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?
