Jougorou Kobato and Yuki Osanai enter high school with a secret pact: to help each other become perfectly ordinary citizens. Both carry the scars of their middle school years, where their exceptional abilities led to painful consequences. Kobato, who refers to his deductive talents as wisdom work, found that his habit of solving mysteries made him resentful and isolated. Osanai, whose fierce and tenacious nature earned her the comparison to a wolf, similarly suffered for standing out. Now they have enrolled at Funato High School in the fictional Kirashi City, a selective public school where they hope to blend in and lead peaceful, unremarkable lives.

Their plan faces an immediate challenge in the form of Kobato himself. Despite his determination to remain a humble and honest citizen, he cannot suppress his detective instincts when faced with a puzzle. Small, seemingly insignificant mysteries keep finding them, from the theft of a bicycle to the question of how a friend managed to make three cups of delicious hot cocoa while dirtying only a single spoon. Osanai, who presents a sweet and innocent exterior, proves equally unable to let things go, particularly when she feels wronged. Her desire for revenge repeatedly threatens to undo their shared goal of ordinariness.

The world around them refuses to cooperate with their aspirations. Classmate Kengo Doujima, a well-meaning but intrusive boy with a strong sense of justice, frequently pulls Kobato into investigations despite his protests. In the first season, the pair navigate incidents such as the mystery of smashed strawberry tarts, the reappearance of Osanai's stolen bike, and a confrontation with a group of thugs that reveals the darker impulses lurking beneath Osanai's calm surface. A blood-red sunset scene in the third episode hints at the true extent of her past and the danger she might pose if she reverts to her old ways.

The second season deepens the exploration of what ordinariness truly means. Kobato attempts to form a normal relationship with a girl named Tokiko Nakamaru, while Osanai becomes entangled with a boy named Takahiko Urino who grows suspicious of her true nature. A series of arson cases in the city forces Kobato back into his role as a detective, and his cold, analytical reaction to discovering Tokikos infidelity reveals just how poorly suited he is for a conventional life. Meanwhile, Osanai orchestrates a devastating psychological takedown of Urino when he accuses her of being behind the crimes, demonstrating that her wolf-like instincts have not diminished but merely gone into hiding.

As the seasons progress, the central question shifts from whether Kobato and Osanai can become ordinary to whether they should even try. Their partnership, initially presented as a practical arrangement for mutual protection, reveals itself as something deeper and more essential. They understand each other in ways no one else can, accepting the sharp edges of their personalities that society rejects. The mysteries they solve, ranging from the recipe for perfect hot cocoa to the truth behind a series of dangerous hit-and-run incidents, serve not as ends in themselves but as windows into the characters' ongoing struggle to reconcile who they are with who they wish to become. The series ultimately suggests that for some people, the pursuit of ordinariness is itself an extraordinary endeavor.