Driven to the verge of extinction by "Aragami," a race of all-devouring monsters, humanity makes its last stand in isolated points of resistance. Invulnerable to conventional damage, only "Oracle Cell" weapons—composed of the same matter which makes up Aragami—can kill these creatures.

However, due to their god-like ability to adapt, the Aragami soon develop further immunity. Having no other hope of fending off the enemy, the remnants of human governments decide to detonate a nuclear reactor and wipe out the monsters facing Eurasia.

The soldiers tasked with this mission are aided by three "God Eaters" dispatched from the Fenrir Far East Branch, an organization controlling what remains of Japan. The state-of-the-art weapons they wield, called God Arcs, are supposedly capable of piercing through Aragami skin and tearing their cores out, pulverizing the monsters. These mighty warriors may just be humanity's last hope of fending off the Aragami threat and averting total extinction.