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!?

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!

Mika received a text. Chisato happened to peek at that text and makes a huge fuss when she suspects that Kusunoki is trying to bring her back to DA! To prevent their plans, the four members of LycoReco join forces to rush the bar where Mika has a secret rendezvous!

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!