In the wake of an earthquake that devastated most of the city, Tokyo has been rebuilt in record time due to the development of humanoid robots known as boomers. After the disaster, these machines now service the city as cheap labor. Genom Corporation is the mastermind behind the boomers, having become so rich and powerful that they have extended its influence into space. However, all is not well with the boomers. Random breakdowns in their neural structure are causing some of them to go berserk, destroying property and killing humans in violent rampages. To combat this, Tokyo has formed the Advanced Police, a peacekeeping force with jurisdiction over boomer matters. There are also rumors of a second group known as the Knight Sabers, a vigilante unit operating from the shadows. Trying to investigate the Knight Sabers, the adventurous Linna Yamazaki travels to Tokyo in pursuit of her heroes. There, she finds the enigmatic singer Priscilla Asagiri, the beautiful entrepreneur Sylia Stingray, and the exuberant Nene Romanova, each with their own reasons for coming together. As the struggle intensifies, the girls learn that the boomer problem might delve deeper than any of them could ever imagine.

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.

No longer concerned with military affairs, Yukichi Fukuzawa intends to act as a lone bodyguard-for-hire, making use of his deadly swordsmanship. However, things are not going as planned for his freelance business, and that is when he crosses paths with a mouthy boy named Ranpo Edogawa. While their initial interactions are intertwined with a bizarre murder mystery, the aftermath prompts the formation of the Armed Detective Agency. Presently, Ranpo finds himself chasing down a gifted individual with the dangerous ability to execute the perfect crime. But as the great detective unravels the case, he soon discovers an elaborate plot to obliterate the Agency in its entirety. Although forewarned of the trap, the Agency continue their pursuit of the criminals, only to end up framed for the crime themselves. Now branded as wanted terrorists, the remaining members must find a way to prove their innocence—even if they must turn to sworn enemies for assistance.