Located on the east side of Tokyo with a commanding view of the destroyed old radio tower, Café LycoReco is a stylish and unassuming establishment that serves as a front for a secret branch of the Direct Attack organization. This is where elite Lycoris agents, trained from childhood as undercover assassins to maintain Japan's artificial peace, carry out missions between brewing coffee and serving dessert. The light novel collects a series of original, self-contained episodes that depict the daily life of the café's staff, focusing on the extraordinary ordinariness found by its two most exceptional agents, the legendary and superhumanly intuitive Chisato Nishikigi and the serious, rule-bound transfer Takina Inoue.

The narrative is framed by the perspective of Kazuhiko, a freelance magazine writer who becomes a regular at LycoReco after being politely denied permission to feature the café in an article. Through his observations and interactions with the eccentric staff, readers are introduced to a series of distinct narrative arcs that explore the characters beyond the main anime storyline. In one tale, Chisato enthusiastically misinterprets Takina's attentive behavior toward a depressed older customer, sparking a comedic misunderstanding that Chisato believes to be a matter of love, much to everyone else's exasperation. Another mission shifts to action when the pair infiltrate a drug-trafficking ring, demonstrating their lethal synchronicity in combat, though Chisato continues to rely on her signature rubber bullets.

The collection moves through a wide spectrum of tones, from lighthearted comedy to surprisingly dark drama. When it is Takina's turn to cook, her rigid and literal-minded approach to nutrition leads to a series of increasingly spartan and repetitive lunches, forcing the rest of the staff to find a delicate way to request a more varied menu without hurting her feelings. The most notable action-driven story, LycoReco of the Dead, presents a zombie apocalypse scenario, either a dream or an alternate reality, where Chisato and Takina must battle their way through a horde to find help. This arc serves as a deep exploration of Takina's subconscious, revealing her growing realization that a world where only she and Chisato remain might not be a terrible fate. However, the narrative does not shy away from the darker implications of their world. A recurring customer, a middle school girl named Kana, is revealed to be suffering from horrific bullying and abuse at school and at home. The story follows a tense, emotional arc as Kana contemplates murdering her tormentors, forcing the LycoReco staff to intervene in a delicate and realistic crisis that contrasts sharply with their usual gunfights. Through these varied episodes, the novel paints a complete picture of the café as a place of refuge, where even agents tasked with killing can find fleeting moments of peace, connection, and a semblance of an ordinary life.