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...!

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 and makes a call to the Port Mafia...

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 by one of the Port Mafia...

Dazai has a face-off with his ex-partner, Chuuya, as Chuuya attempts to uncover Dazai's true intentions for letting himself get captured. Meanwhile, Atsuhi faces Akutagawa's intense and inexplicable hatred for him, as the ship continues on to the meeting place where he will be handed off in exchange for the bounty on his head...

Francis, the leader of The Guild, a North American organization of gifted members, is the one responsible for the bounty on Atsushi's head. Fukuzawa refuses Francis's offer to buy out the Agency, but their agents begin to disappear...

The Port Mafia's council of five top executives has decreed that Mimic must be annihilated. In the ensuing battle, Odasaku has a fateful encounter with Gide, the leader of Mimic, who makes a cryptic prophecy. Night falls, and the usual bar now awaits Dazai, Odasaku and Ango...

Mori, the leader of the Port Mafia, sends a letter to Margaret M. and Nathaniel H., threatening to destroy them and the ship they are protecting.

Atsushi is abducted onto the Moby Dick. Meanwhile, Lovecraft succeeds in capturing Q. Francis F. and the Guild prepare to carry out what they call their "emergency plan."

Atsushi and Akutagawa fail to call off the Moby Dick's descent. They search desperately for other ways to protect Yokohama.

Port Mafia leader Mori Ougai orders a fifteen-year-old Dazai Osamu to investigate the appearance of a certain individual in the Yokohama Settlement area.

Nakahara Chuuya and Dazai Osamu reveal the truth behind Arahabaki, Randou, the former Port Mafia boss and Chuuya himself.

The café that the Detective Agency members frequent is attacked by The Park, who are after the Guild’s property.

The gifted responsible for the virus is on the run as Nakagawa Atsushi and Akutagawa Ryunosuke chase after him. Meanwhile, the Detective Agency has the Rats’ hideout surrounded to try to capture Fyodor Dostoevsky.

Suspecting that Lucy is cooperating with the terrorist organization known as the Armed Detective Agency, Jouno and Tetchou pay a visit to the cafe at where she works, in hopes of tracking down Atsushi and Kyouka.