Japan has become a wasteland devastated by the Rusty Wind which causes all things to rust away. A suspicious looking priest visits a checkpoint all alone, yet on his back rests a bow priests wouldn't use. Meanwhile, Milo, a doctor running a clinic in the town of Imihama, is researching new medicines in secret in order to save his older sister, Pawoo, who's being corroded by the Rust. But that day a stranger appears before him...

With the information obtained from Tetsujin Town, Bisco and Milo continue to head north. As they make their way through Shimobuki Prefecture, the land encased in snow, they encounter Tirol, nearly frozen to death. With Tirol's aid, the two continue their journey toward their final destination - Konakidani, the land said to contain the Rust Eater.

Bisco and Milo finally reach Konakidani when the Pipe Snake, a divine beast with two heads that's the size of a dragon, appears before them. That's also when Pawoo catches up to them with the worst possible timing. Soon enough, even Pawoo is dragged into the intense battle against the Pipe Snake. Meanwhile, Kurokawa also closes in around them...

Bisco is gravely wounded by the shot from Kurokawa. Milo leaves him behind to storm into enemy territory and rescue his captured friends, Pawoo and Jabi, but Kurokawa awaits with meticulously set traps. During their confrontation Kurokawa reveals his great ambition and the secret behind the Mushroom Keeper's persecution.

Milo is left standing at death's door by Kurokawa's traps. Kurokawa has once again captured Jabi, and this time he shares a glimpse of his terrifying plan to utilize Tetsujin, the very same defensive weapon that covered all of Japan in the Rust Wind. It seems like no one can stop Kurokawa, and yet at the very moment Jabi feels that despair, a familiar face appears before Kurokawa...