A hiveminded alien force reengages war with Tatsumiya Island years after Kazuki led a team of mech pilots to destroy them. In an explosive battle over the fate of humankind, the young warriors risk everything to save their only home from assimilation.

Kazuki shot the Mir in First Operation Azure in the Arctic 2 years ago. Since then, broken Mirs have been acting in each their own way. Although Kazuki quitted a Fafner pilot due to low vision, he still believes that vanished Soshi will get back home. On the day of Bon Festival, Michio and Yumiko's daughter Miwa predicts that a naval vessel drifts ashore in Tatsumiya Island. The prophecy comes true, a boy Misao is in the vessel. He knows about vanished Soshi because he is a Festum.