June 25, 2150. One of the few surviving locations on Earth populated by humans, Hawaii, was attacked by Festums. The Neo United Nations declared ROE Alpha, burning the island and all its survivors to ashes.

The Fafners are deployed to save a Human Army transport craft from a Festum. It's the first battle in two years, but Hiroto, Rina, Akira, Sui, and Maya are all smiles as they calmly board the Fafners. They dominate the battle until the experienced Festum unleashes an attack style they've never seen before, leaving the five pilots at a loss. Then unexpected reinforcements arrive...

Mitsuhiro and the other Human Army pilots visit the café Rakuen on Tatsumiyajima. Billy excitedly devours his curry and Ai takes notice of Kazuki, while Mitsuhiro keeps a close eye on the scene and Maya watches them all with a thoughtful expression. Miwa has met Emery and the two happily converse in some special way that only they understand, while Miwa's mother, Yumiko, watches with concern. Meanwhile, Fumihiko is shocked by the information offered by General Narain. A frightening situation that could change the world's balance of power is pressing closer.

Three new pilots have been chosen: Mikado Reo, Kaburagi Sui, and Mikagami Mimika, third-year students at Tatsumiyajima Middle School and juniors to Kazuki and the other pilots. They have received more advanced genetic manipulation than the previous pilots, and each has unique strengths. Hazama Yuuko and Canon prepare their mechs, but the new pilots are dissatisfied with their colors and names... Meanwhile, Fumihiko and Chizuru have the difficult job of notifying the new pilots' families of their children's new placement.

A giant Azazel-type Festum, called a Walker, attacks Tatsumiyajima, having been observing the island since Emery arrived there. The Walker blasts the shields open and sends Sphinx-types and other Festums inside.

The expeditionary force, carrying Miwa, arrives at the Srinagar base in India. Towering to the heavens in Srinagar is the World Tree, the Mir revered by the Esperantos. Miwa insists that she wants to speak to it right away, but...

Festums cause chaos by attacking Srinagar, the base where the Tatsumiyajima expeditionary force is stationed, from both inside and outside. Maya runs to Yumiko and Miwa, but is shocked when she sees what Miwa looks like after trying to make contact with a Festum.

The pilots of Tatsumiyajima are struggling more than they expected in the battle when a new power suddenly springs forth. Sui is left terrified after a brush with death, Reo is frustrated after losing in a sword battle, and Seri begins to doubt the very fact that she's alive.

Srinigar is on the verge of destruction after an attack from an Azazel-type. Emery and the others put up a mental wall to defend the World Tree, but it only causes the Festums to corrode their minds.

Sein and Nicht rush to destroy the Azazel-type attacking the World Tree. Kazuki shows the boundless power of Sein with its limiters removed, and Soushi expertly manipulates the "uncontrollable" Nicht. Their overwhelming power stirs excitement in the Human Army soldiers as well as the Tatsumiyajima pilots.

Sui and the other pilots left behind on Tatsumiyajima are going about their individual lives. It appears that the SDP, the phenomenon that occurred during their previous battle to vastly amplify their Fafners' powers, has only influenced them positively.

An unknown phenomenon has surfaced in all the pilots from the island. It's clearly an effect of the Fafners' new core, but the Alvis medical team has no idea if it threatens their lives or not, much less how to treat it. Though, Orihime seems to know something about this...

A group of emigrants who strayed from the main party have been attacked by Festums. The Fafner unit, excluding Kazuki and Soushi, rush to help, but Kazuki insists that the two of them should have gone out in Sein and Nicht.