"The Detective Is Already Dead" centers around Kimihiko Kimizuka, a high school student who inadvertently becomes entangled in a world of mystery and danger after a chance encounter with Siesta, a brilliant detective. Siesta, who claims to be a "legendary detective," recruits Kimihiko as her assistant during a flight, marking the beginning of their partnership. Together, they tackle a series of bizarre and dangerous cases, often involving supernatural elements and shadowy organizations. Their adventures span the globe, with each case revealing more about Siesta's enigmatic past and her connection to a mysterious entity known as SPES.

The narrative alternates between two timelines: the present, where Kimihiko is trying to live a normal life after Siesta's death, and the past, which chronicles their time working together. In the present, Kimihiko is drawn back into the world of espionage and mystery when he encounters Nagisa Natsunagi, a girl who bears a striking resemblance to Siesta and possesses her heart. Nagisa seeks Kimihiko's help to uncover the truth behind her connection to Siesta and to confront the remnants of SPES, a criminal organization tied to Siesta's demise.

Key characters include Kimihiko, whose ordinary demeanor belies his resourcefulness and loyalty; Siesta, the charismatic and enigmatic detective with a tragic past; and Nagisa, whose presence reignites Kimihiko's involvement in the world of intrigue. The series explores themes of loss, identity, and the lingering impact of past relationships, as Kimihiko grapples with his memories of Siesta and his evolving bond with Nagisa. The plot intertwines action, mystery, and emotional depth, with each case contributing to the overarching narrative of uncovering the truth behind SPES and Siesta's legacy.