Nothing has been the same ever since the Festum invaded the island. While the population copes with constant attacks and battle preparations, the leaders of Alvis struggle to move forward under increased political pressure from the Neo UN. Meanwhile, battle fatigue has set in for the young pilots and, while Kazuki is away on a rescue mission, Shoko is pressed into service to pilot the Fafner with devastating results.

The team is in the fight of their lives when the Festum attacks them on a mysterious island. Koyo goes on a rescue mission and saves the day but at a great personal cost. After the dust settles the remaining pilots try to get on with their lives as best they can but Kazuki's mind wanders back to his childhood and to an unpleasant memory involving Soshi.

After he is taken hostage, Kazuki learns once and for all that he has been partially assimilated with the Festum. During his captivity at the Neo UN base he is reunited with his mother, but all is not as it seems since Festum assimilated Kazuki's real mother when he was just a child. He has precious little time to ponder this mystery as the Neo UN launches a full-scale military takeover of the Tatsumiya island.

Control over Alvis takes center stage and Fumihiko, Commander Barnes and Mizoguchi play a strategic high stakes game of nuclear engagement. Just as the Neo UN begins to withdraw from the island Commander Barnes asserts his authority over all of his subordinates and launches a nuclear missile towards the island.

The battle-weary pilots finally start to relax, only to be interrupted by yet another Festum invasion. As disaster looms, off-season blooms and the first sign of natural conception in 30 years spark hope for the island's survival. Meanwhile, Sakura hides a devastating secret as Festum attacks become increasingly strategic and complex.

Before Kazuki's very eyes, Soshi is kidnapped by a Festum along with the Siegfried System. In order to rescue Soshi, the remaning pilots of the Tatsumiya Island join forces with the Human Force in an all out battle against the North Pole Mir...

The youth of Tatsumiya Island lived ordinary lives, but their peaceful existence was all a lie. The invasion of the Festum, the shining golden enemy, transforms their peaceful island into a high-tech military fortress. The beginning of a whole new Fafner, this novel includes the thoughts of Soshi, Maya, Shoko and more that didn't appear in the anime series along with battles of the Fafner and Festum.

Tatsumiya Island is a small, idyllic haven for those lucky enough to call it home... until a surprise attack by a savage enemy shakes the water-locked paradise to its core. With Festum on the warpath, it's up to the island's dedicated inhabitants to pilot powerful Fafners and fight back! Before the gun smoke clears, illusions will be shattered and lifelong friendships will be stretched to their limits. Will this peaceful island survive the chaos of all-out war?

The never-ending clash between Fafners and Festum rages on, but new confrontations are stirring behind the scenes. After a shocking conversation with Soshi, Kazuki decides to risk his safety and explore the outside world for himself. But will the newfound knowledge that he and Soshi must communicate in order to help humanity evolve eventually lead to reconciliation or total chaos?