A 15-year-old boy travels back in time—over 1,200 years ago to the Heian period—and faces a war between oni (demons) and humans in the former Japanese capital of Kyoto.

In a future governed through the lens of a camera, where people eat synthetic food and pursue an online existence in lieu of physical contact, a group of children begin meeting up in the real world. The aloof Ayumi Kono, the genius hacker Mio Tsuzuki, and the socially awkward Hazuki Makino set out to find the fourth member of their group, Yuko Yabe, who has gone missing. With the help of Myao Rei, an unregistered citizen proficient in martial arts, they are able to find Yuko. However, when their situation takes a sudden turn for the worse, the group stumbles headlong into a dark mystery that challenges everything they know about their world.

Silent Sky is a combination of the additional episodes 13 and 14. It consists of the story in the future, three months after the incident that was similar to "New Generation Madness" and the disease Chaos Child Syndrome that brought by the past earthquake in Shibuya.

The film takes place on a certain isolated island, at a certain middle school, and on the eve of the culture festival. A boy quits baseball after playing his whole life and has a fight with his best friend. Then, they suddenly meet a mysterious, red-eyed girl named Noruda, and a huge typhoon hits the middle school.