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.

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.