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...

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.