On its way to the Far East Branch, the transport plane from the Russian Branch is attacked by a huge flock of smaller-sized Aragami. The plane’s passenger is Alisa, a New-Type God Eater like Lenka. The 1st Unit is ordered to bring her back safely, but Alisa flatly refuses. The team is determined to guard her and render assistance when suddenly, Aragami reinforcements appear and the situation takes a turn for the worse. Lindow and Lenka set out to rescue Alisa, but she rejects them. Why is Alisa so adamant about not leaving the transport plane...?

Lenka returns from the successful mission to rescue Alisa and is assigned to the 1st Unit along with Alisa and Kota. He goes into the city for the first time at Kota’s invitation and learns of the existence of Aegis Island which is faintly visible on the water surface in the distance.

Lenka is frustrated to learn that the Aegis Project has a long, long way to go. In order to complete the project, massive amounts of the natural resource known as Oracle must be harvested from the Aragami. As Lenka stands dumbfounded, Soma kicks him out of the way and tells him, “What we can do is hunt Aragami. That’s all.” The veteran God Eaters, Lindow and Soma, are away when the next assignment comes in, so Sakuya, who has been left in charge, decides to hunt lesser Aragami. But knowing that the bigger the core, the faster the Aegis Project can be completed, Lenka suggests that the mission target large-type Aragami. When Kota and Alisa both agree with Lenka, Sakuya decides to take three rookies on a hunt for the large-type Aragami…Vajra.

Lenka, Alisa, Kota and Sakuya are out on a mission to hunt two large-type Aragami known as Vajra when they encounter an unusual black Vajra that devours even its own species. This Vajra is ridiculously powerful and the 1st Unit ends up scattered. Lenka takes Alisa who has lost consciousness and escapes into an abandoned building. His God Arc is fractured and Lenka’s confidence takes a serious blow. Alisa, who also loses her God Arc in the fray, is overcome with terror as childhood memories of her parents being killed by the black Vajra come flooding back. But it’s not over for the battered and wounded duo as a pack of Ogretails threateningly advance toward them in the abandoned building where they sought refuge.

Lenka and Alisa are rescued from a violent attack of Aragami, then taken by Lindow to Asyl (asylum), a place where people who were turned away at the Fenrir Far East Branch refugee center live and support each other. Making the rounds with Lindow, Lenka comes upon a shocking sight. Lenka is unable to answer when Lindow pointedly asks why he wants to destroy Aragami. A Vajra appears and moves threateningly toward Asyl, and Lindow orders Lenka to “Go back and protect everyone. No one is to die...including yourself.

Lenka and Alisa make it back to the Fenrir Far East Branch. But Alisa suffers from post-traumatic stress and Lenka’s God Arc is badly damaged, so they are put on temporary leave. Flashbacks of her battle with the variant Vajra, the brutal Dyaus Pita, continue to haunt Alisa, and her inability to conquer her fears frustrate her. When Lindow questions why powerful Aragami are heading toward the Far East region, Tsubaki shows him data which shocks him. Meanwhile, Dr. Sakaki looks into how Lenka’s God Arc could possibly be broken. And despite the lack of both New-Types, the Branch Director is about to begin a new battle strategy.

A change is occurring in Lenka’s body due to over-adaptation to the Oracle Cell. Lenka is in a dilemma when told that while he cannot escape inevitable death, if he resigns as a God Eater, he may be able to prolong his life for a little while. Meanwhile, a briefing is being held on the “Meteorite Strategy,” the crucial mission necessary to execute the Aegis Plan. Lenka’s tactical skills have been recognized and he is appointed a leader. Lenka learns that members of other units avoid Soma who has been labeled a “shinigami” (harbinger of death) and is told by Sakaki, “Fate is cruel... It can be said both you and he are its victims.” Soma’s hidden past is revealed to him, but Lenka...

Fifteen years ago, the Utsugi family finds an abandoned baby and decide to take him in. They name the infant Lenka, and he is raised lovingly by his adoptive mother, father and older sister Iroha. They live in Agir, a refugee commune. One day, Lindow Amamiya, a God Eater, appears and encourages everyone to take the patch test. Anyone testing positive is considered to have attributes of a God Eater, and will be allowed into Fenrir, including any blood-related kin. Lenka's father despises this discriminatory method of selection. However...

Operation Meteorite, a plan to lure Aragami with a newly developed guiding device, is critical to the completion of the Aegis Plan. Lenka is unable to join the unit due to adjustments that must be made on his God Arc, but Lindow recommends him to command the advance base camp. Alisa rejoins the unit, but the others seem to feel uncomfortable around her. Operation Meteorite starts successfully, but suddenly the Aragami turn away from the guiding devices and head northwest. Lindow is sent to do reconnaissance and realizes that the Aragami are converging on Asyl, the settlement that Lindow has been helping.

There is a high possibility that the irregularity in the guiding devices may have been due to internal hacking. Surrounded by Vajra, Lindow continues his lone battle. Lenka acquires a new God Arc and gets Lindow out of harm's way in the knick of time. Reasoning that someone must have set another guiding device that suddenly distracted the Aragami, Lindow sets out to find and destroy it. But Deus Pita appears before him. It is an uphill battle for Lenka and Lindow, but the 1st Unit arrives to help.

Leaving Lindow to deal with Deus Pita, Lenka and the others rush to Asyl to rescue the people there. But Pita catches up to them, with Lindow's bracelet hanging from its mouth... The 1st Unit is in shock, but they have no time to waste. Suddenly, Pita threatens the safety of Asyl. Lenka beseeches the members of the 1st Unit to remember Lindow's wish and his orders, and inspires the team with his words, "Believe in your friends! Destroy it!"