Chisato Nishikigi and Takina Inoue spend their days balancing two very different lives. By night, they operate as agents of Lycoris, a secret government organization of female assassins working to eliminate crime and terrorism in Tokyo. By day, they work as waitresses at Café LycoReco, a small establishment in Sumida that serves as a front for their operations.

The light novel focuses on the everyday adventures and misadventures of these two agents alongside their colleagues. Chisato, the cheerful and highly skilled agent known for using rubber bullets and her superhuman ability to dodge gunfire, wants to show Takina the joy of watching a movie in theaters. However, an important mission comes up right before showtime, forcing them to juggle their personal plans with their duties as secret agents.

Another incident finds Takina waking up in a cabin in the woods, uncertain of her circumstances, while a murderer lurks nearby. The novel also explores what other Lycoris agents like Fuki Harukawa, Takina's former team leader, and Sakura Otome, her replacement, do when they are not actively protecting the city from the shadows.

The story expands beyond Chisato and Takina to include the full cast of LycoReco. The skilled hacker Kurumi, also known as Walnut, continues to live and work at the café after faking her death. Mika, the Afro-Japanese manager and father figure to Chisato, oversees the team, while Mizuki Nakahara, a former intelligence division member desperate to get married, helps with missions and café operations. As an episodic slice-of-life narrative, Recovery Days delves into the bond between the pacifistic Chisato and the more serious Takina, showing how their partnership develops through daily challenges. It also highlights their interactions with supporting characters like Fuki and Sakura, offering a more relaxed and character-driven look at their world compared to the high-stakes main storyline of the anime.