"If you order me to, Master, I'll wipe out all of humanity."
SORD (Social Ops, Research & Development) is an agency that was established to recruit and train talented operatives for special anti-terrorism units. All kinds of misfit girls are enlisted in SORD's training schools. They are issued guns and live ammunition in the name of national defense, for that is the only way they could be granted a place in the world.
Arata is the handler of Class D at Mihama Academy, a school for SORD. Class D is nicknamed "Dead Stock", because it's full of third-rate students. In order to increase his students' chances of survival, Arata trains them using PeTS, an experimental neural signal synchronization technology.
During one extrajudicial mission, he finds a mysterious girl sleeping inside an incubator at a terrorist hideout. As if drawn together by fate, Arata is able to sync with her using PeTS, and the two narrowly escape with their lives. The girl introduces herself as "L", and Arata welcomes her into Class D.
These events trigger the beginning of Class D's fight against the mysterious terrorist organization "Hadeo."
This is a story of girls who, with nowhere else to go, have chosen the path of the gun...
