"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 being recruited as an assistant to Siesta, a brilliant and enigmatic detective. Siesta, a silver-haired girl with exceptional deductive skills, is a member of a secret organization tasked with combating global threats. Together, they embark on a series of missions to solve complex cases, often involving supernatural elements and criminal conspiracies.

The narrative unfolds through a mix of present-day events and flashbacks, revealing the duo's past adventures. Siesta and Kimihiko share a close bond, with their partnership forming the emotional core of the story. However, their time together is cut short when Siesta dies during a mission, leaving Kimihiko to grapple with the loss and the unresolved mysteries she left behind.

Years later, Kimihiko encounters Nagisa Natsunagi, a girl who bears a striking resemblance to Siesta and claims to possess her heart, which was transplanted into her body. Nagisa seeks Kimihiko's help to solve a new wave of cases, reigniting his connection to the world of detectives and forcing him to confront his past. As they work together, Kimihiko uncovers deeper layers of the organization Siesta belonged to and the true nature of the threats they face.

The series explores themes of loss, identity, and the lingering impact of past relationships. It blends elements of mystery, action, and emotional drama, with a focus on the evolving dynamics between Kimihiko, Nagisa, and the memory of Siesta. The plot is driven by intricate cases, unexpected twists, and the gradual unraveling of the overarching mystery surrounding Siesta's legacy and the organization's hidden agenda.