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.

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...

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!"