Yukichi Fukuzawa, who is no longer interested in military matters, plans to work as a lone bodyguard for rent, using his lethal swordsmanship. However, things in his freelancing business are not going as he had hoped, and at that point he meets Ranpo Edogawa, a brash young man. The Armed Detective Agency is founded as a result of their interactions, which are first entwined with an odd murder investigation.
Ranpo is now on the hunt for a talented person with the deadly capacity to carry out the ideal crime. But as the brilliant detective works to solve the case, he soon unearths a complex plan to completely destroy the Agency.
Despite being aware of the trap, the Agency continues to hunt down the culprits, only to find themselves falsely accused of the crime. The remaining members must find a way to establish their innocence, even if that means turning to their sworn foes for help. They are now listed as wanted terrorists.