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 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.

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...

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!"