Driven out from his orphanage, Nakajima Atsushi wanders the streets of Yokohama on the bring of starvation. Determined to live, a chance encounter with a drowning stranger changes his fate...

The Agency investigates a series of disappearances in Yokohama. Kunikida enlists the help of a hacker named Taguchi Rokuzou, but all they find are photos of the victims and mention of a mysterious figure called the Azure Messenger. They follow the trail of clues to an abandoned hospital...

Following the Azure Messenger's bomb threat, the Armed Detective Agency must race to prevent the deaths of hundreds, which would taint the Agency forever. However, Dazai's seemingly distracted by Sasaki Nobuko, the lone survivor of their raid on the abandoned hospital...