Kafka Hibino has almost abandoned his dream of joining the anti-Kaiju "Defense Force." He now works in Kaiju clean-up, disposing of the bodies of slain Kaiju and thinking back with regret to the days he spent with his childhood friend Mina Ashiro, captain of Defense Force's Third Division.

After turning into a Kaiju, Kafka is forced to flee. His escape is interrupted, however, by the arrival of another Kaiju...

It's time for Kafka's first mission, and he witnesses the true power of the Defense Force when a Kaiju strikes a nearby city.