A decade before the formation of the Armed Detective Agency, a young Yukichi Fukuzawa works as a brooding ronin, a bodyguard for hire in the criminal underbelly of Yokohama. He accepts a routine assignment at a local theater, but the job spirals into chaos when a patron is murdered under bizarre circumstances. Before Fukuzawa can fully assess the scene, an arrogant and eccentric teenage boy named Ranpo Edogawa appears, casually solves the murder in seconds, and displays a genius-level intellect that he claims is a supernatural ability. This incident forces the reluctant bodyguard to take the strange boy under his protection.

The narrative follows the unlikely duo as they investigate a complex death threat against a theatrical troupe. Ranpo, who possesses no actual supernatural power but rather an unparalleled gift for deductive reasoning, insists on using the case to prove his talent. As they dig deeper, they uncover a plot involving a high-stakes kidnapping orchestrated by a mysterious organization known as V (or Five), which operates with deadly efficiency in the shadows of Yokohama. The investigation forces Fukuzawa to confront the corruption within local police institutions, particularly when the officer escorting Ranpo, Mitamura, is revealed to be the perpetrator. While Ranpo uses himself as bait to calculate the timing of Fukuzawa's rescue, the bodyguard must rely on his martial prowess and burgeoning sense of duty to save the boy.

The story serves as the origin arc for the Armed Detective Agency, adapting the third light novel of the Bungo Stray Dogs series. Key narrative beats include the duo’s confrontation with the shadowy organization V, where they first encounter figures like Fyodor Dostoevsky, and their eventual meeting with the enigmatic intellectual Soseki Natsume. Natsume, the man they were sent to protect, reveals the trap was a test, ultimately entrusting Fukuzawa with a "skilled business permit" to establish an agency where Ranpo can operate freely. The manga explores themes of justice versus institutional corruption, detailing how Fukuzawa transitions from a detached mercenary to the stoic founder of the Armed Detective Agency, driven by his paternal bond with the young genius Ranpo.