Takina Inoue is a member of a government-sponsored all-female task force of assassins and spies made up of orphans known as "Lycoris", an undercover group (named after the flower) who eliminate criminals and terrorists in Tokyo while disguised as high school students to maintain peace in Japan, with roots in a fictional pre-Meiji group named "Higanbana". However, during an operation to intercept a large exchange of firearms, she starts firing indiscriminately at the enemies in order to save a colleague who was taken hostage, jeopardizing the safety of other Lycoris in the process. As a result, the agency dismissed her for disobeying orders. She was then transferred to work with an elite Lycoris agent Chisato Nishikigi, who is known for her involvement in the destruction of the old radio tower, on a branch of the agency which operates undercover as a café called "LycoReco". Intending to be reinstated back to the agency, Takina cooperates with Chisato on managing the café, while the peace that is being protected by the Lycoris is being challenged by terrorists led by Majima.