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'. This new incarnation of Mihama Academy is home to a diverse group of students, who every day work to polish their unusual skills - sometimes on the job. Mihama now entrusts the misfit girls who attend it with guns and live ammunition. Paying their own safety no heed, these students are again and again plunged into dangerous extrajudicial missions - all for the good of the realm. "We've been granted a place in the world. That alone isn't enough - there wouldn't be any meaning in living, if that was all we had... It's not enough just to get by on the backs of others. I live by my own strength, and I fight to survive. Because only the survivors among us belong with the living..." 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 students 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... “You're right. There's a reason we need to get back... even if it means crawling home on our hands and knees.” “Let's meet up again someday... if we're still alive.” And introducing Sengoku Ayame - Sengoku Ichiru's brother, and a handler at St. Aile's: “If takin' her in alive's too much of a challenge, just get rid of her - I don't give a damn. I wanna see this mess cleaned up.” What answers will Tohka find? She has the truth in her sight...