Season 2

Dustin killed Kamal in Dacca. Kamal told him that Dustin's brother Jimmy is in Perseus Company now as his last words. Meanwhile, Festum has attacked the moving camp again and again, the number of casualties have been increasing day by day.

The Neo-UN force attacked the camp under ROE Alpha. They captured Mk-V with Hiroto while Kazuki and Soshi fought against Festum. After the withdrawal of them, Narein decides that the camp moves toward the Pacific through Khabarovsk area.

Olga send a report to Tatsumiya Island. The side-effects of Canon and Sakura are getting worse. However, Canon continues to use her SDP for getting a great future. Sui finally tells his mother what he really thinks.

Alvis finds out why the crystals of Gordius in Urd are getting bigger. Kenji also finds out a clue to control the side-effects. Canon finishes to plan new model of Fafner, but her weight has already decreased to 21 grams.

Alvis finds out what the enemy's Mir evolved into. Then, Festum appears, and launches a severe attack on the island. Meanwhile, 3 spies under Dustin try to assassinate Kazuki in the camp.

Alvis senior members collapse because Festum begins to encroach on Mir of the island. Mechanics built a new model of Fafner in a hurry while Alvis young members consider an escape plan, Division Phase Exodus. And Kenji and Sakura get married in order to reassure Sakura's mother.

Koyo gets back to the island. Kenji gets his SDP. Fafner pilots regain their strengths, but the price they pay is too much. Meanwhile, Akira is mentally worn out. Narein uses Festum to escape from Argos Platoon.

The camp have been paying a big sacrifice in each battle due to a shortage of commodities. Finally, they arrive at the shore of the Pacific, and then, they find an artificial bird which made by Alvis.

It continues three-sided fight between the Neo-UN force, Festum, and Fafner team under Tatsumiya Island and Perseus Company. Misao and his Mir support Fafner team. Argos platoon captures Mark-VII and Maya during the battle.

Gallop reveals Jonathan's true identity, and she forces Maya to launch their Fafner Mark-Raison. Mizoguchi and Soshi go to negotiate with the Neo-UN for the release of Maya. General Burns tells Mizoguchi what Gallop really plans. Meanwhile, the Boy incites hatred of Jonathan.

Alvis approaches the 3rd Alvis aka Wadatsumi Island. When they starts the landing operation, Festum appears with hidden hostility. Akira, Rina and Sui make strenuous efforts to beat Festum, but Vagrant in orbit moves. Meanwhile, Kazuki chooses his way of life.

Altair is coming closer to the Earth. The Boy uses General Burns and surviving members of Argos Platoon to monopolize the power of Altair. Emery tries to take root Asoka in the 3rd Alvis. Soshi feels that he is near his end.

Alvis discloses all the information to coexist peacefully with Mirs to the fleets of Neo-UN. Mark-Raison shows its tremendous power, so Fafner team have a hard fight. When everyone on the battlefield see the falling Altair, Orihime orders Alvis to execute Division Phase Exodus.