Grisaia: Phantom Trigger is set several years after the events of The Fruit of Grisaia. At this point, Mihama Academy, once a sanctuary for girls, has been repurposed as a training school by SORD, focused on developing talent for national defense. The students, each with their own specialized skills - Rena and Maki with firearms expertise, Tohka and Gumi as skilled snipers, Chris handling explosives and data, and Murasaki as a ninja for intelligence - take on complex cases beyond the capabilities of the police or Self-Defense Forces.