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, a 32-year-old man, is unsatisfied with his job as a sweeper. From a young age, he has aspired to join the Defense Corps and kill kaijuus for a living. After a few failed attempts, however, he gave up on his dreams and resigned himself to the mediocrity that provided a decent paycheck. Nevertheless, when an ambitious, 18-year-old recruit named Leno Ichikawa joins his cleaning team, Kafka is once again reminded of his desire to join the military.

Following a chain of unfortunate events and an interaction with the junior sweeper, 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.

The year is 2045, and artificial intelligence has undergone tremendous developments. Governments use them as weapons, engaging in never-ending warfare to sustain their economies. The mercenary group GHOST, headed by Major Motoko Kusanagi, is no stranger to this landscape. However, the rapid innovation of this technology causes a new threat to loom over the horizon.
Having left Public Security Section 9, Kusanagi and her group are involved in many operations worldwide related to these proxy wars. But a seemingly simple job of locating an arms dealer drags GHOST into a hidden conflict against cybernetically enhanced individuals, who have inexplicably gained extreme intelligence and physical abilities. Dubbed “post-humans,” their emergence sets off a chain of events leading to the reunion of Section 9. Armed with a new mission, it is up to Kusanagi and her reestablished team to prevent global chaos at the hands of these post-humans.