Mysterious living beings named Aragami suddenly appear on Earth and begin to devour everything in sight. Determined to destroy every single Aragami, a youth comes to Fenrir Far East Branch. His name is Lenka Utsugi. Immediately, Lenka and his fellow enlistee, Kota Fujiki, begin rigorous God Eater training under their instructor, Tsubaki Amamiya. Itching to take part in real battles, Lenka’s wish unexpectedly comes true when Aragami infiltrate the Far East Branch. Even as anxiety heightens in the strategy room, Lenka’s resolve grows stronger.

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...?

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.

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!"