With the highest kaiju-emergence rates in the world, Japan is no stranger to attack by deadly monsters. Enter the Japan Defense Force, a military organization tasked with the neutralization of kaiju. Kafka Hibino, a kaiju-corpse cleanup man, has always dreamed of joining the force. But when he gets another shot at achieving his childhood dream, he undergoes an unexpected transformation. How can he fight kaiju now that he's become one himself?!

Mina Ashiro falls into the clutches of Kaiju No. 9 after its emergence in Tachikawa. Kafka goes to rescue her, but daikaiju start emerging in several places across the city, impeding his progress. The situation becomes even more complicated when he picks up on a new kaiju presence and a never-before-seen entity reveals itself!