Two years have passed with no incident since Soshi came back home. Kazuki and his generations quitted Fafner pilots, they are working in new position now. The next generations have been growing up as good Fafner pilots or good cadets. One day, Perseus Company led by General Narain brings a girl Emery with an important information to the island. The incident has an effect on the next core's growth.

Festum shows up after Perseus Company. The next generations and Maya fight against Festum with the support of Fafner corps in Perseus Company. After that, Miwa and Emery meet for the first time, but they already have been good friends because of their ability.

Kazuki gets a shock to hear why Fafner pilots in Perseus Company can operate Fafner. Jonathan reveals his identity to Maya. General Narein and Commander Makabe share the information about Altair, they have a constructive meeting. Alvis decides that they allow Emery to contact with island's Mir though the sleeping next core.

Sui, Reo, and Mimika get promoted regular pilots. Canon names new 3 Fafners. Jonathan meets Miwa and Yumiko for the first time. Akira wants to enlist in the detachment to fight with Perseus Company, but Rina is against him strongly. Kazuki begins to be able to see Tsubaki holding a baby in a vision.

The detachment led by Mizoguchi left for Srinagar to bring Miwa and Emery with Perseus Company. It includes Hiroto, Akira, Maya and their Fafners, Miwa's mother Yumiko. Festum attacks Tatsumiya Island again. Sui finds them something strange, so he asks Soshi to change the operation.

The detachment arrives at Srinagar. It's a big town where refugees live. There is a big Mir, Asoka, like a big tree at the center of the town. Meanwhile, the next core wakes up in Tatsumiya Island, she orders Kazuki and Soshi to protect Miwa with Mk-Sein and Mk-Nicht.

Festum suddenly makes a raid on Srinagar just after Asoka forced Miwa to grow up her body and power. Several hours before that, Festum attacked Tatsumiya Island with an overpowering strength. Fafner pilots and Kenji in Siegfried System got into a desperate situation.

Five Fafner pilots in Tatsumiya Island gained a new power named Super Demension Phenomenon. Alvis began to investigate about changed Urd, and considered how to send Kazuki and Soshi with their Fafners to Srinagar even just a little faster.

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.