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. Takina is enthusiastic about returning to DA now that she's buddied up with the super-elite No. 1 Lycoris (?) Chisato, but her job at LycoReco is just one weird thing after another!?

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. The members of LycoReco work together to help Walnut escape, but a violent group of armed assailants attacks Chisato and the others…!?

Chisato reluctantly went to DA Headquarters for a health checkup and physical fitness test. When Takina heard, she decided to tag along to make a direct request for reinstatement at DA. With Chisato, Takina negotiates, but their commander will hear none of it. Moreover, 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. On one particular day, Chisato noticed that Takina's underwear is ■■■■■…! 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. Chisato and Takina, who were requested as bodyguards and guides, go all out to support Matsushita's Tokyo sightseeing tour! Meanwhile, Takina learns a curious fact about Chisato!?

An outbreak of serial attacks against Lycoris occur. In order to stay in groups, Takina decides to stay over at Chisato's house. But for these two, living with someone for the first time is full of unpredictable situations!? Meanwhile, Kurumi secretly searches through the information DA is holding and gets close to the surprising truths about the assaults on Lycoris.

After learning that Café LycoReco is in the red, Takina decides to take charge of accounting on her own. Takina flawlessly breaks down everything from indiscriminately restraining Chisato from wasting bullets to shadowing the café's members. She even goes as far as planning a new menu item. But the menu item has a shape that’s too terrible to put into words!?

Chisato's artificial heart was targeted. Now that the battery can no longer be charged, the remainder of Chisato's days are set. Kurumi, who chases down clues about the irreplaceable artificial heart, asks Mika about what happened back then. Meanwhile, Chisato is summoned to Headquarters as DA prepares for a large-scale operation to suppress Majima.

Chisato breaks the news that she will shut down Café LycoReco so that Mizuki and Kurumi do not get caught up in her personal affairs. Around the same time, Takina, who returned to DA, uses Majima as a stepping-stone to track down Yoshimatsu in order to save Chisato's life. They finally captures Majima's client and infiltrates their hideout…!?

The Lycoris of DA stormed the Enkuboku to stop Majima. Just before the operation, Takina rushes to Café LycoReco when Kusunoki informs her that they cannot get in contact with Chisato. However, after receiving threats from Robota, Chisato and Mika set out to rescue Yoshimatsu, who is being held hostage...

Chisato is dragged into a tough fight against Majima at the old radio tower, but Takina rushes in just in the nick of time. Meanwhile, the existence of the Lycoris is exposed to the public due to Majima's ploy. At Headquarters, Kusunoki's command is stripped, and a decision is made to dispose of the Lycoris inside the Enkuboku!?

All is settled with the incident at Enkuboku—or so it seems until Majima, who should have been defeated at the old Radio Tower, reappears before Chisato. Majima planted a bomb in the Enkuboku, betting on the explosion when he challenges Chisato to a one-on-one fight. As Chisato's own time limit approaches, the final battle begins!