The story picks up immediately after the events of Grisaia no Meikyuu, with Kazami Yuuji having been detained for suspected involvement with an international terrorist organization, lead by Heath Oslo, that has managed to enter Japan's borders with a devastating new weapon of mass destruction in hand. Meanwhile, at Mihama Academy, the remaining students find themselves with time running out - due to financial issues, the school is set to close within the month. Over the past year, though, the girls of Mihama have finally begun to find their own legs, thanks to Yuuji's involvement - are they really just going to bury their heads in the sand and let the world change around them? And are they really willing to let the man who changed their lives slip away without so much as trying to win him back? As the end of their time at Mihama Academy approaches, Amane, Makina, Sachi, Yumiko, and Michiru find themselves arriving at a single conclusion.