To maintain its image as a crime-free paradise, the Japanese government operates a secret organization known as Direct Attack or DA. This agency recruits young orphaned girls, training them as off-the-books operatives called Lycoris who are tasked with eliminating criminals and terrorists before the public ever becomes aware of a threat. Disguised in school uniforms to blend into everyday life, these agents are skilled assassins authorized to use lethal force to uphold the nation's artificial peace.

The story centers on Takina Inoue, a cool-headed and efficient Lycoris who values results above all else. During an operation to intercept a major firearms deal, a colleague is taken hostage. In her determination to save her partner, Takina defies orders and opens fire indiscriminately on the enemy. Her actions, though successful in saving her comrade, are seen as insubordinate and reckless by DA's leadership, as they could have jeopardized the secrecy of the organization. As punishment, she is transferred from the main headquarters to a remote branch office.

This branch operates under the guise of a café called LycoReco in Tokyo, run by a man named Mika. There, Takina is forced to partner with Chisato Nishikigi, who is considered the greatest Lycoris agent of all time. Where Takina is serious and pragmatic, Chisato is a free-spirited optimist and a staunch pacifist. Despite her incredible combat abilities, she refuses to kill her opponents, instead using specialized non-lethal rubber bullets. The café itself takes on a wide variety of odd jobs for the public, ranging from babysitting and shopping to teaching Japanese, in addition to the secret missions assigned by DA.

Takina views her assignment to LycoReco as a temporary setback and is determined to prove herself so she can return to the main organization. However, she soon discovers that Chisato is not just a skilled agent but also the only Lycoris to hold the rank of ensign, distinguished by a red uniform. As they are thrown into chaotic everyday situations and dangerous missions, their contrasting philosophies constantly clash. Takina believes in the efficient elimination of threats, while Chisato demonstrates that there is always another way.

Their peaceful, if unusual, life at the café is challenged by a rising terrorist threat led by a deranged man named Majima, who seeks to expose DA and destroy the false peace it protects. The story follows the mismatched duo as they work alongside other café employees, including Mizuki, a former DA intelligence operative, and Kurumi, a genius hacker known as Walnut. As the conflict escalates, Takina learns the painful reason for Chisato's pacifism: she possesses an artificial heart that keeps her alive, and her time is limited. The narrative arc traces Takina's growing emotional connection to her new partner, forcing her to re-evaluate her loyalty to the organization that discarded her and ultimately choose to save her friend, even if it means defying DA for good.