Kimihiko Kimizuka teve sua vida mudada quando se tornou assistente de um misterioso detetive conhecido como “Siesta”. Após alguns anos de missões e casos alucinantes sendo resolvidos junto a ela como seu assistente, Siesta subitamente morreu, deixando para traz Kimihiko, que voltou a sua vida tediosa de estudante. Agora no ensino médio, Kimihiko precisa aprender a lidar com o seu dia a dia sem as agitações das investigações, mesmo que seu passado com Siesta fique voltando para o provoca-lo, muito graças a irmã mais nova da detetive.
Kimizuka, a middle-school student, meets the beautiful detective Siesta in the process of thwarting a plane hijacking. As they next investigate a mystery at Kimizuka’s school Culture Festival, Siesta urges Kimizuka to become her sidekick.
Kimizuka is approached by Nagisa Natsunagi, a girl with a yearning seemingly inspired by the heart she received in a transplant. When Kimizuka asks Fuubi for help, she takes them to meet an unexpected someone who provides surprising information.
A teen idol, Yui Saikawa, enlists Kimizuka and Natsunagi--who has taken up the mantle of legendary detective--to guard a priceless sapphire. In preparing for this, the two realize that more than just a precious jewel is at risk.
On the night of Yui Saikawa’s big stadium show, Kimizuka and Natsunagi struggle to protect her from a hidden assailant. But the further the two dig into the plot against Saikawa, the clearer it becomes that the teen idol has secrets of her own.
Siesta and Kimizuka investigate a series of murders by someone called Cerberus, who for some sinister reason steals victims’ hearts. As Cerberus eludes Siesta’s pursuit, she comes up with a more desperate tactic, much to Kimizuka’s dismay.
Siesta takes an extreme risk to stop Hel and her mutated terror-beast, and pays a price for her courage. The outcome halts the fight against SPES, at least temporarily. In the wake of this battle, Kimizuka makes a surprising discovery in an alley.
While Siesta convalesces, Alicia takes on the role of substitute detective and seeks the Eye of Sapphire, with Kimizuka’s assistance. When at last Siesta recovers, recovered, the three celebrate, but this celebration takes an unexpected turn.
Siesta has recovered and is eager to press forward with pursuing the serial killer and SPES. Alicia, however, insists on being involved, and as the two clash and sparks fly, the mystery of Alicia's identity comes more sharply into focus.
In an attempt to rescue Alicia, Siesta, Kimizuka, and Char set off to confront Hel and SPES on their home ground. There, they encounter one alarming surprise after another and come to realize that with SPES, nothing is as it seems.
Saikawa, Natsunagi, and Kimizuka set off on a cruise together, during which Kimizuka unexpectedly encounters a former acquaintance. It turns out that something precious is onboard the ship, something which attracts the wrong sort of attention.
Facing off against Chameleon with Natsunagi’s life on the line, Kimizuka finds that he is not alone in this battle, with help coming in unexpected forms. But against this wily foe, Kimizuka’s allies--and his own resilience--are tested to the limits.
Siesta, returned in spirit, partners with Kimizuka in a desperate battle against an ever-changing and resilient foe. In the aftermath of this battle, the survivors carry lingering questions and doubts, and must try to find closure amongst themselves.