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 Rat. After losing his special privileges, including the right to live in Chronos, Sion now lives in Losttown with his mother, Karan. One day, Sion is working as a supervisor at a park, when he discovers the body of a dead man. The corpse appears to be of an elderly man, but Sion soon learns that the body belongs to a man who was in his thirties, and this fact is being concealed by the city authorities. The next day, Sion's co-worker, Yamase, is also transformed into an old man instantaneously before dying. Immediately after this happens, Sion witnesses a bee clawing its way out of Yamase's neck.

Sion gives up everything he has to escape No. 6 with Rat. They manage to arrive safely at Rat's home, but it isn't long before a black blister appears on Sion's neck, just like the one that was on Yamase's. Sion is in a great deal of pain, but Rat is able to save his life. However, his body has been completely transformed. Later, Sion and Rat analyze the black blister. They discover that it is the pupa of a special "bee" that infests human bodies and matures at a rapid rate.

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.

Another person in No. 6 has suddenly aged and died. Sion hears about this from Rikiga and races to the theater where Rat is performing to inform him of the news. This is the first time he's seen Rat act. But during the play, Rat is visited by a strange wind and song and he faints on stage. Meanwhile, in an art museum in No. 5, Safu is looking at a work which displays three bees when she, like Rat, is visited by a strange wind and song, and she also faints.

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.

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?