The Pretty Boy Detective Club has three rules for membership: Be pretty; Be a boy; Be a detective. Mayumi Doujima, despite being none of the above, finds herself joining after helping the PBDC undercover a national conspiracy involving a detonated nuclear bomb she witnessed as a child. Mayumi now crossdresses as a boy and sharpens her detective skills unraveling more mysteries such as the middle school underground casino bar or the death of the school president.