For years, Japan has faced the threat of enormous, Godzilla-like creatures known as "kaijuu." To safeguard the population, an elite military force called the Defense Corps takes on the perilous task of confronting these monsters.

After a kaijuu is defeated, specialized personnel known as "sweepers," who work for the Professional Kaijuu Cleaner Corporation, are responsible for disposing of the remains. Kafka Hibino, a 32-year-old sweeper, is dissatisfied with his current role.

He has always dreamed of joining the Defense Corps to fight kaijuus directly, but after several unsuccessful attempts, he settled for the steadiness of his current job. His ambition is reignited when he meets Leno Ichikawa, an ambitious 18-year-old recruit who joins his cleaning team.

Following a series of unfortunate events and an encounter with Ichikawa, Kafka is infected by a parasite-type kaijuu, which transforms him into a humanoid monster. Armed with his new abilities, Kafka decides to pursue his long-held dream of joining the Defense Corps.