Yumi et Kyo sont des enfants qui ont été sélectionnés pour participer à une mission top secrète, pour être les pilotes des premières unités de combat Fafner ; la dernière chance de survie pour la race humaine. L'ennemi est impitoyable, sans remords et capable de lire dans l'esprit des humains. C'est pourquoi les détails de cette mission sont gardés secrets, même pour le personnel concerné. Les jeunes pilotes doivent faire appel à tout leur courage et à leur foi pour survivre et mener à bien leur mission, faute de quoi le destin de l'humanité serait compromis.

Nous ne disposons d'aucun synopsis. Votre contribution est la bienvenue !

Nous ne disposons d'aucun synopsis. Votre contribution est la bienvenue !

The year is 2148. Two years after the end of the original Fafner in the Azure TV series, Tatsumiya Island and its surviving residents have returned to some semblance of recovery. However, things have become desperate for our hero, Kazuki; nearly blind now, and partially crippled from his battles with the Festum two years earlier, he clings to the promise his fallen friend Soushi made to him to return to the island and set things right again. Kazuki's hopes flare when a lifeform is detected within an unmanned submarine that comes floating into Tatsumiya Bay one night, but the person aboard isn't Soushi; it is a mysterious "boy" named Misao Kurusu who may not be entirely human, and who claims to have been sent by Sōshi. With Misao's arrival, hostilities break out anew between the Human Army and the Festum, and the Fafner pilots are thrown into the most desperate battle of their lives - this time, with the fate of TWO races riding on their shoulders.

Kazuki, Maya, Kenji, and Canon, all accompanied by Kyouhei, charge straight towards the entrance of the core in order to rescue Soushi, who is revealed to be inside the core. During the operation, Tsubaki is experiencing the death process to complete the learning process for the Festums to understand life and death. Moreover, she will need to return to the core to complete this process. Kenji maps out a plan of attack, Canon confirms the battle formations, and Maya reminds that all pilots will return back to the island alive. Soushi is being controlled by Idun, who uses the Siegfried System to exploit the weaknesses of the pilots, that being to break their battle formation.

Les quatre pilotes se réunissent pour vaincre Idun ensemble. Pendant ce temps, Tsubaki lutte contre ses émotions en quittant l'île pour se synchroniser avec le noyau de l'île.