Grisaia: Phantom Trigger takes place after the existing Grisaia trilogy, and features a completely new group of heroines as well as a new protagonist.

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. There's a gunslinger called Rena (nickname: "The Rabid Dog"), a sniper named Tohka, a demolitions expert called Chris, a spy named Murasaki, and finally, Haruto, their handler. Together they make up an agency called SORD (Social Ops, Research & Development). The specialist training school now entrusts the misfit girls who attend it with guns and live ammunition in the name of national defense.

Paying their own safety no heed, these students are again and again plunged into dangerous extrajudicial missions - all for the good of the realm.