After the incidents involving Heath Oslo, the existence of the Japanese-American counter-terrorist organization, known as CIRS, is now public knowledge. CIRS was rebuilt from the ground up and its more hidden functions were transferred to a new agency: SORD (Social Ops, Research & Development). The main purpose of SORD is to train a new generation of spies to defend the country from future threats. To achieve its ends, the organization has built many schools in the country. Mihama Academy, abandoned after its sudden closure, has become a specialized training school. So, this new Mihama Academy is home to different groups of students who every day work hard to improve their skills. These students put their own safety at risk by immersing themselves in various extrajudicial missions, all for the good of the country.

Following the Heath Oslo incident, the existence of the US-Japanese anti-terror organization CIRS has become a matter of public knowledge. CIRS has been rebuilt from the ground up, and its most covert functions spun off to a new agency: SORD (Social Ops, Research & Development). The goal of SORD is to train a new generation of operatives to defend the country against future threats. To that end, the organization has established a series of schools up and down the country. Mihama Academy, more-or-less left to rot after its abrupt closure, has been given new purpose as one such 'specialist training school'. It now entrusts the misfit girls who attend it with guns and live ammunition. No matter how much life grinds them down, what future awaits these girls, who've themselves chosen the path of the gun?

While Rena and Maki recover from their injuries, the other SORD members jet off overseas for a school trip. Within moments of their arrival, though, the Mihama gang are pulled into a manhunt for a SORD deserter, assisted by student Sylvia and Velvet of St. Aile's International School. Tohka's the star of the show this time round, but she's wrestling with her own issues - old memories of her parents, and a promise to a friend that she wasn't able to keep...