Grotesque, Godzilla-like monsters called "kaijuu" have been appearing around Japan for many years. To combat these beasts, an elite military unit known as the Defense Corps risks their lives daily to protect civilians. Once a creature is killed, "sweepers"—working under the Professional Kaijuu Cleaner Corporation—are left to dispose of its remains.

Kafka Hibino is a 32-year-old member of the Professional Kaiju Cleanup Corp. Kafka was also childhood friends with Mina Ashiro who he made a vow with to join the Defense Force together and protect Japan from Kaiju. However, Kafka failed the entrance exam numerous times and quit on his dreams of being a member of the Defense Force while Mina went on to become the captain of the Defense Force’s 3rd Division.

Following a chain of unfortunate events and an interaction with an ambitious recruit named Leno Ichikawa, Kafka encounters a parasite-type kaijuu that forces its way in through his mouth—turning him into a humanoid monster. With his newfound powers, Kafka aims to give his lifelong dream a final try.