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

Despite joining the Armed Detective Agency, Nakajima lacks conviction that he'll be of any use. Just as he's about to bid the agency farewell, a bomber takes over the agency with one of the agency employees as his hostage!

After passing the entrance exam and becoming an official member of the Agency, Atsushi is assigned to his first case with Tanizaki and Naomi. Though deceptively simple on the surface, there's more to the case than meets the eye.

Though saved from the Port Mafia by Dazai's intervention, Atsushi feels responsible for bringing trouble to the Agency's door. Rather than risk another attack because of him, Atsushi decides to leave the Agency.

After repelling the Port Mafia's Black Lizards with deceptive ease, Atsushi is tasked with assisting Rampo on a case. Skeptical of the self-dubbed great detective who seems to lack all common sense, Atsushi is about to witness Rampo's ability first-hand.

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 mentions of a mysterious figure called the Azure Messenger.