"Lycoris Recoil" is set in a world where Japan maintains peace through a covert organization known as the Direct Attack (DA), which employs highly trained young girls called Lycoris to eliminate threats before they escalate. These operatives blend seamlessly into society, posing as ordinary schoolgirls while carrying out missions to protect the nation. The story centers on Chisato Nishikigi, a cheerful and exceptionally skilled Lycoris, and Takina Inoue, a disciplined and serious operative reassigned to Chisato's team after a mission goes awry.

Chisato operates under a unique philosophy, prioritizing non-lethal methods and valuing life above all else, which contrasts sharply with the DA's usual approach. Her optimistic demeanor and unorthodox tactics often clash with Takina's by-the-book mentality, creating a dynamic partnership. As the two work together, they uncover deeper layers of corruption within the DA and face off against a mysterious hacker group known as Alan Institute, which seeks to destabilize the organization.

The narrative explores themes of trust, morality, and the cost of maintaining peace through covert operations. Chisato's past and her connection to the enigmatic Alan Institute come to light, revealing her as a key figure in a larger conspiracy. Takina, initially focused on regaining her position within the DA, gradually questions the organization's methods and aligns more closely with Chisato's ideals. Together, they navigate a web of intrigue, confronting enemies both within and outside the DA while forging a strong bond as partners.

The series balances action-packed sequences with moments of character development, delving into the personal struggles and growth of its protagonists. Supporting characters, such as Mika, Chisato's mentor, and Kurumi, a skilled hacker, add depth to the story, providing both assistance and insight into the challenges faced by the Lycoris operatives. The plot builds toward a climactic confrontation that tests the limits of Chisato and Takina's partnership and their commitment to their ideals.