Two generations of the Nonezawa family – Asafumi and his wife Shizuka, and Asafumi's grandfather Rentarō and his Malayan lover Saya – are connected across the years by the mysterious Mandala Road, which simultaneously casts Asafumi and Rentarō from their respective ages into a haunting post-apocalyptic world. As becomes apparent, Asafumi, Rentarō, Saya, and Shizuka are all, in their own way, on a private journey to discover and reconcile themselves with their memories of violence, both seen and experienced, as they struggle to understand themselves, unearth the emotions they have repressed, and learn to live with a past that seems always to be too close behind them.

In the present day, a young married couple, Asafumi and Shizuka are trying to start a new life, having had to move after losing their jobs. Asafumi decides to join the family business of selling medicines, and a notebook that used to belong to his grandfather Rentarō leads him to explore the mysterious Mandala Road in the hopes of finding his grandfather's former customers. Shizuka, meanwhile, struggles to resign herself to her new role as a housewife and wonders if she made the right choice in marrying Asafumi.

Following the end of World War II, Saya, a woman from a Malayan native tribe, is on her way to Japan with her seven-year-old son to find Rentarō, who was her wartime lover and the father of her child. When she arrives, however, she discovers that Rentarō has another family and has no place for her. Haunted by memories of torture from the Japanese seeking information about Rentarō and the abuses she suffered working in a brothel, Saya tries to rebuild her life and learn to live with her past.

Both setting out alone on Mandala Road in two different time periods, Asafumi and Rentarō wake up one day having both entered a post-apocalyptic world, where the people seem to have mostly been wiped out by a mysterious "calamity" and the ones that remain are scarcely human. Asafumi, Rentarō, Saya, and Shizuka are all, in their own way, on a private journey to discover and reconcile themselves to the memories of violence, both seen and experienced, as they learn to live with a past that seems always to be too close behind them.