真壁一骑是个生长在对日本而言十分乡下的龙宫岛上的少年──对他来说，像这样的和平是普通到不能在普通的状况。 但当由硅所构成的不明生物·异界体（Festum）开始攻击龙宫岛时，他才开始注意到他现在所拥有的和平生活不过只是个被创造出来的假象。 为了取回自己的和平生活，他和同伴开始一起搭乘人类所创造出来的巨大兵器·法夫那（Fafner）和异界体战斗── 在激战的彼端，等待着他的是……

Yumi Ikoma and Ryou Masaoka are children who have been selected to take part in a top secret mission, to be the pilots of the first Fafner combat units; the last chance of survival for the human race. The enemy is ruthless, remorseless and is able to read the minds of humans. Therefore, the details of this mission are kept a secret even from the personnel involved. The young pilots must use all their courage and faith in order to survive and complete their mission or the fate of mankind would be compromised.

The year is 2148. Two years have passed since the world was defended from the mysterious Festum, leaving the world in peace. Soushi promised Kazuki that he would one day return to Tatsumiya Island but instead he still keeps himself hidden, living his life in the peace that he created. But one day a mysterious ship arrives at Tatsumiya Island... a ship with nobody but a single sleeping girl on board. The peace isn't going to last as long as everyone might hope...