A small island of Tatsumiya, is located off the coast of Japan, quietly tucked away and it all seems calm and peaceful, until a sudden attack is made by the enemy - Festum. Enter Kazuki; who knows that he must pilot a Fafner in order to defeat Festum. Kazuki is successful, but shortly after the attack it is revealed that the island is artificial. It then begins to move around the ocean in an attempt to evade not only Festum, but the rest of humanity.

As a result of the continuous attacks, many of the youth on the island must be trained as Fafner pilots, but Kazuki is the most skilled and qualified. Can the youth of Tatsumiya continue to withstand these brutal attacks by the Festum or will they be destroyed altogether?