Five years ago Shinjuku was wiped out from a giant explosion in a certain incident. In one corner of the ruined city lies the Yoshimi Detective Agency, Japan's one and only detective agency specializing in bugs. One day, he gets involved with a strange case. The woman who requested he search for the stink bug, Mari tells him that he is actually the legendary loose-cannon detective who used to be her lover and disappeared after the Shinjuku incident. What was the explosion for? Who the heck is the detective??