Away from home for 10 years, Azuma Kazuki had no idea what was awaiting him upon his return. He certainly did not expect to be attacked by dozens of heavily armed people and taken as their prisoner. Fortunately, Azuma's stay in captivity is short. Wielding a strange sentient weapon—known as Bubuki—upon her right arm, his childhood friend, Kogane Asabuki, rescues him. After escaping, Azuma learns that he too has the power to control Bubuki. Together with his new companions, he must revive the Buranki titan named Oubu, that sleeps somewhere deep underground. With this knowledge and purpose, a new path to unearth the truths behind the Buranki opens before Azuma.

Following the conclusion of the three-way organizational war, government bureaucrat Ango Sakaguchi recalls an event that transpired years ago, after the death of the former Port Mafia boss. Osamu Dazai, still a new recruit at the time, was tasked with investigating rumors related to a mysterious explosion that decimated part of the city years ago—and its connection to the alleged reappearance of the former boss. Due to circumstances out of his control, he is partnered with Chuuya Nakahara, the gifted yet impulsive leader of a rival clan known as the Sheep, to uncover the truth behind the case and shine a light on the myth of Arahabaki—the god of fire who might just lead Dazai to the case's solution. Meanwhile, in the present day, it is business as usual once again for the Armed Detective Agency. Their peaceful break will not last for long, however, as enemies old and new gather their strength and prepare for another face-off.

Despite their differences in position, three men—the youngest senior executive of the Port Mafia, Osamu Dazai; the lowest ranking member, Sakunosuke Oda; and the intelligence agent, Ango Sakaguchi—gather at the Lupin Bar at the end of the day to relax and take delight in the company of friends. However, one night, Ango disappears. A photograph taken at the bar is all that is left of the three together. Fast forward to the present, and Dazai is now a member of the Armed Detective Agency. The Guild, an American gifted organization, has entered the fray and is intent on taking the Agency's work permit. They must now divide their attention between the two groups, the Guild and the Port Mafia, who oppose their very existence.

A large-scale catastrophe is occurring across the planet. Ability users are discovered after the appearance of a mysterious fog, apparently having committed suicide, so the Armed Detective Agency sets out to investigate these mysterious deaths. The case seems to involve an unknown ability user referred to as Collector, a man who could be the mastermind behind the incident. Trust and courage are put to the test in order to save the city of Yokohama and ability users across the world from the grip of Collector where the Armed Detective Agency forms an unlikely partnership with the dangerous Port Mafia.