Mamiya Hibiki is a sincere young man with a bright personality. He works as a car mechanic and lives with his girlfriend, Ogasawara Kurumi. They have dated since they were high school students. Hibiki makes a plan to propose to Kurumi. On the day he proposes to his girlfriend, he slides off a tunnel and becomes trapped. 4 days later, he is able to escape, but he faces a different world. There are no people outside, the traffic system is destroyed, and there are bloodstains on the streets. What happened to the world? Hibiki tries to find Kurumi.

As a new community, the "House of Hope" has appeared. Who are they with a prosperous civilization? In addition, a golem with an "x" that seems to have been artificially attached appears. A new threat comes to those who survive the "End-of-world".

Hibiki and Yuzuki set out on a journey to find Kurumi, Hibiki's lover who disappeared with a mysterious group called "X" while pregnant with his child despite being infected with the golem virus. During their long and grueling journey, Hibiki and Yuzuki almost give up, wondering if they will ever see Kurumi again. They arrive in Salito, the holy place of the "Emblem of Light," a religious group that aims to create a new world after the devastation of the Golem.

The story takes place 20 months after the end of Season 3. Hibiki has lost his friends and loved ones who fought alongside him, and even his beloved child, Mirai, has been taken from him. Wounded with wounds all over his body, Hibiki wanders alone through the apocalypse, only to be rescued by the Niiyama Foundation Group led by Asuha. When he is reunited with his former companion Kanae, she cannot hide her surprise at seeing Hibiki as a different person. At the Niiyama Foundation Group, Hibiki obtains the information that Mirai is in "Utopia," which is rumored to be the last city of hope for mankind.