Takina Inoue, a secret agent who protects the security of Japan called a "Lycoris," is ordered to transfer to the café LycoReco in consequence of a certain incident.
LycoReco received a request from the top hacker, Walnut. He wants help fleeing the country from other hackers in the same business who are all after his head.
Chisato reluctantly went to DA Headquarters for a health checkup and physical fitness test. With Chisato, Takina negotiates, but their commander will hear none of it. Her ex-partner Fuki is teaming up with a new companion.
After the incident at DA Headquarters, Chisato and Takina live a smooth and easy life at LycoReco. Fed up with Takina's absolute indifference toward herself, Chisato decides to take her shopping.
The client this time is Matsushita, a man whose body is connected to a machine. Knowing his time is short, Matsushita returns to his homeland of Japan for some sightseeing. Meanwhile, Takina learns a curious fact about Chisato!?
After increasingly violent attacks directed at Lycoris take place, Takina moves in with Chisato. Majima ambushes Chisato, and learns of her ties to the Alan Institute.
Majima, recovered from the explosion, enacts the next part of his plan. Chisato and Takina stalk Mika at a fancy restaurant, but find him with a surprising companion.
LycoReco closes down, and Chisato is told the reason why she is still alive. Takina and the DA head to Enkuboku Tower to intercept Majima, who plans to expose the Lycoris to the world.
The DA's activities are exposed to the world by Majima as citizens discover the Lycoris in their midst. Takina leaves the DA to help Chisato. Kurumi discovers an important secret regarding Chisato's heart.
Chisato finds Yoshimatsu, who tells her that the only way she can get her heart back is to kill him. The DA work with Walnut to dispel Majima's accusations.
