In the not-so-distant future, a catastrophic event has turned the old capital of Japan into a wasteland, forever changing the lives of its people. Decades later, three schoolgirls set foot into the now forsaken city.

The girls encounter a man searching for his missing child. Hearing that the child may have wandered into a dangerous area, the girls rush to find the child before it’s too late.

Vice Principal Mishima learns from the rescued Tanizaki about a man known as the Delivery Man believed to be their leader. Meanwhile, the girls follow a lead that unexpectedly takes them to the Delivery Man himself.

The Coppelion succeed in bringing down the monster crow, which then crash-lands in one of the Zones. When the girls arrive at the site, they discover that a company named YELLOW CAKE is responsible for dumping high-level waste into the Old Capital.

While heading to their next destination, the girls encounter a father and his pregnant daughter being attacked by a group of armed men.

Aoi’s careless action results in her being captured by the 1st Division. Realizing that the enemy is actually after the Coppelion and not the survivors, Ibara tries to rescue Aoi, only to be knocked unconscious by one of the men.

Ibara is critically injured after getting caught in a blast caused by the 1st Division’s tank. Thanks to the efforts of Haruto and Taeko, Ibara manages to pull through, only to learn that a guilt-ridden Aoi has now secluded herself.

Haruto informs the group that a massive and lethal Zone is approaching the Planet. With time running out, Ibara comes up with a last-ditch plan to evacuate everyone from the area using an old abandoned train.

The Coppelion set their escape plan into motion by dividing into two teams, with the Diversion Team led by Ibara, who is tasked with drawing the Ozu Sisters’ attention away from the others.

The Diversion Team find themselves in serious trouble when the 1st Division brings out their secret weapon, the Iron Spider. As Ibara tries to hold off the Ozu Sisters, Aoi is left with the task of stopping the Iron Spider alone…

Ibara and the Diversion Team are nervously waiting for the train to arrive when they are attacked yet again by the Ozu Sisters. After a fierce battle, Ibara manages to fend off the sisters and make it on board the train.

Ibara and the other passengers rejoice after their train has successfully escaped from the Zone. But their celebration is cut short when they see a vengeful Kanon chasing after them in the Iron Spider, which they thought had been destroyed.