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.