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?!

Kaiju No. 9 shows up to steal the power of Kaiju No. 2, wielded by Isao Shinomiya, director general of the Defense Force. At the end of the deadly battle, Isao manages to get No. 9 on the ropes, but he ends up exhausting all his strength, allowing the kaiju to steal No. 2's power. With Isao defeated, No. 9 fuses with the director general and takes on Kafka, Kikoru, and Narumi! Will they be able to defeat No. 9 and save their fearless leader?!