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.