"God Eater" is set in a dystopian future where humanity faces extinction due to the emergence of monstrous creatures known as Aragami. These beings are nearly indestructible, feeding on all life forms and resistant to conventional weapons. To combat this threat, the Fenrir organization develops specialized weapons called God Arcs, which are the only effective means of fighting Aragami. These weapons are wielded by individuals known as God Eaters, who possess unique abilities to bond with the God Arcs and harness their power.

The story centers on Lenka Utsugi, a young recruit who joins Fenrir's Far East Branch to become a God Eater. Lenka is driven by a personal desire to protect others and avenge the loss of his family to the Aragami. His journey begins with rigorous training and the challenge of adapting to the God Arc, which requires a strong will and compatibility. Lenka's determination and resilience quickly set him apart, earning him the attention of his peers and superiors.

The narrative unfolds as Lenka and his fellow God Eaters, including the experienced Alisa Ilinichina Amiella and the stoic Soma Schicksal, undertake missions to defend humanity's last strongholds. Alisa, a skilled but emotionally scarred fighter, struggles with her past and the psychological toll of her battles. Soma, a veteran God Eater, harbors a mysterious connection to the Aragami and grapples with his own identity. Together, they form a team that must confront increasingly powerful Aragami while uncovering the truth behind the creatures' origins and Fenrir's hidden agendas.

As the story progresses, the God Eaters face not only external threats but also internal conflicts within Fenrir. The organization's experiments and secrets come to light, revealing the ethical dilemmas and moral compromises made in the fight for survival. Lenka and his comrades must navigate these challenges while maintaining their resolve to protect humanity. The series explores themes of sacrifice, camaraderie, and the human spirit's resilience in the face of overwhelming odds.

The plot builds toward a climactic confrontation with the Oracle Cells, the source of the Aragami's power, as the God Eaters strive to find a way to end the threat once and for all. The series balances intense action sequences with moments of character development, delving into the personal struggles and motivations of its protagonists. Through its narrative, "God Eater" presents a compelling exploration of humanity's fight for survival in a world on the brink of collapse.