Taking place in the year 2148, the residents of Tatsumiya Island are still recovering from the aftermath of the original Fafner in the Azure TV series. Nonetheless, the protagonist, Kazuki, remains distressed due to his blindness and partial disability from previous conflicts with Festum. Despite this, he clings to the promise made by Soushi to return to the island and fix everything. His hope is reignited when an unmanned submarine carrying an unknown lifeform enters Tatsumiya Bay one night. However, much to his surprise, the person inside is not Soushi, but rather an unusual "boy" named Misao Kurusu. Misao reveals that he was sent by Soushi and admits to being more than just a human being. Unfortunately, with his arrival, conflict resurfaces between the Human Army and the Festum, compelling the Fafner pilots to engage in their toughest battle yet. This time, the fate of two races lies in their hands.