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.
Despite joining the Armed Detective Agency, Nakajima lacks conviction that he'd 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.
Now an official member of the Agency after passing their entrance exam, Atsushi is assigned to his first case right away with Tanizaki and Naomi. Though deceptively simple on the surface, there's more 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.
Following the Azure Messenger's bomb threat, the Armed Detective Agency must race to prevent the deaths of hundreds. However, Dazai's seemingly distracted by Sasaki Nobuko, the lone survivor of their raid on the abandoned hospital.
Dazai goes missing, but the Agency operatives feel it's just business as usual. Meanwhile, Atsushi accompanies Yosano Akiko on a shopping expedition, where they are suddenly plunged into the middle of a terrorist bomb threat!
Kyouka was made into an assassin by those who abused her ability, and Atsushi can't help but feel sympathy toward her. Unable to turn her in to the military police, Atsushi ends up taking her out on a date. Meanwhile, Akutagawa is busy berating his former supervisor--Dazai
Dazai has a face-off with his ex-partner, Chuuya, as Chuuya attempts to discover why Dazai let himself get captured. Meanwhile, Atsuhi faces Akutagawa's intense and inexplicable hatred for him.
In the aftermath of Atsushi and Dazai's abduction, the Agency must decide what to do with Kyouka. Meanwhile, the Port Mafia also deliberates what to do with Akutagawa, now comatose, as his enemies seek vengeance.
