25 de junho de 2150. Um dos poucos locais sobreviventes na Terra povoados por humanos, o Havaí, foi atacado por Festums. As Neo Nações Unidas declararam ROE Alpha, queimando a ilha e todos os seus sobreviventes até as cinzas.

Os Fafners são enviados para salvar uma nave de transporte do Exército Humano de um Festum. É a primeira batalha em dois anos, mas Hiroto, Rina, Akira, Sui e Maya sorriem enquanto embarcam calmamente nos Fafners. Eles dominam a batalha até que o experiente Festum desencadeia um estilo de ataque nunca visto antes, deixando os cinco pilotos perdidos. Então chegam reforços inesperados...

Kazuki fica chocado ao saber por que os pilotos Fafner da Perseus Company podem operar Fafner. Jonathan revela sua identidade para Maya. General Narein e Comandante Makabe compartilham informações sobre Altair, eles têm uma reunião construtiva. Alvis decide que eles permitem que Emery entre em contato com Mir da ilha através do próximo núcleo adormecido.

Sui, Reo e Mimika são promovidos como pilotos regulares. Canon nomeia novos 3 Fafners. Jonathan conhece Miwa e Yumiko. Akira quer se alistar no destacamento para lutar com a Companhia Perseus, mas Rina é fortemente contra ele. Kazuki começa a ver Tsubaki segurando um bebê em uma visão.

O destacamento liderado por Mizoguchi partiu para Srinagar para trazer Miwa e Emery com a Companhia Perseus. Inclui Hiroto, Akira, Maya e seus Fafners, a mãe de Miwa, Yumiko. Festum ataca a Ilha Tatsumiya novamente. Sui acha algo estranho neles, então pede a Soshi para mudar a operação.

A força expedicionária, transportando Miwa, chega à base de Srinagar, na Índia. Elevando-se aos céus em Srinagar está a Árvore do Mundo, o Mir reverenciado pelos Esperantos. Miwa insiste que quer falar sobre isso imediatamente, mas...

Os Festums causam o caos ao atacar Srinagar, a base onde a força expedicionária Tatsumiyajima está estacionada, tanto de dentro quanto de fora. Maya corre até Yumiko e Miwa, mas fica chocada ao ver a aparência de Miwa depois de tentar fazer contato com um Festum.

Os pilotos de Tatsumiyajima estão lutando mais do que esperavam na batalha quando um novo poder surge repentinamente. Sui fica apavorado após um encontro com a morte, Reo fica frustrado depois de perder em uma batalha de espadas e Seri começa a duvidar do fato de ela estar viva.

Srinagar is destroyed by Festum. When the most of them prepare for the worst, 2 heroes come flying. Meanwhile, Dustin of Argos Platoon suggests to Commander Kamal of Dacca Base that Neo-UN should issue ROE Alpha to Srinagar.

Kazuki and Soshi crushed Festum, and they saved the people who were almost assimilated. After the battle, Narein decides that his army takes Miwa, Emery and diminished Asoka to an other safe place with surviving refugees.

When Fafner pilots in Tatsumiya Island and Orihime spend time to relax, Alvis has a meeting about SDP and the change of Urd. Then, the pilots begin to use their each SDP without Fafner, but show terrible side-effects.

The camp are moving toward Dacca Base behind scheduled. Festum becomes to be able to assimilate using radio signals. Kamal decides to send reinforcements to the camp.

The Secretary-General of the Neo-UN, Gallop, wants to exterminate Festum and the people who having a Mir gene as soon as possible. General Burns feels antipathy to her. Meanwhile, the pilots in the island are afraid that fighting will make their side-effects worse.

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.