Yumi and Kyo 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.

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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.

The four pilots all reunite and defeat Idun together. Meanwhile, Tsubaki struggles with her emotions at leaving to synchronize with the island core. Kazuki, with the help of Akane, manages to rescue Soushi, bearing the assimilation. As the Meir begins to make its way to the atmosphere, Maya snipes at it, preventing it from spreading all over the world. Tsubaki has become one with island, as she dissolves into thin air. Idun, barely alive in the Fafner Mark Nicht, hinders Kazuki and Soushi from leaving the battlefield, but Koyo is able to save the two. On their way to the island, Soushi vanishes because of his near assimilated state.