Several years after The Fruit of Grisaia… What was once "Mihama Academy," a sanctuary for young girls, has now been transformed into a SORD (Special Organization for Research & Development) training school dedicated to fostering talent for national defense. Rena and Maki specialize in firearms, Tohka and Gumi excel at sniping, Chris handles explosives and data processing, and Murasaki is a skilled ninja for intelligence operations. Together, they take on cases too complex for the police or Self-Defense Forces, repeatedly facing dangerous missions. This is the story of these young girls, painted in blood and gunpowder.