Depiction of Japan's economy, based on Shoutarou Ishinomori's epynomous manga.

Kivotos is a federal megalopolis comprising thousands of schools and is led by the General Student Council (GSC), which acts as its governing body. Ironically, despite being an academy city, Kivotos is rife with gun violence, and all students wield firearms as part of their everyday lives. As if the crisis in Kivotos was not enough, the GSC president is nowhere to be found. Fortunately, before her sudden disappearance, the GSC president enlisted the help of Sensei—a teacher who is most likely the only one in Kivotos—to support students in their time of need. Sensei's first course of action is to assist Abydos High School, a once prestigious academy now with merely five students in attendance. These remaining students are doing everything they can to pay their academy's crippling debt of almost one billion yen.

Hoping for a fresh start, househusband Masaki Fujiyoshi, his spouse Hiromu, and their toddler son, Hikari, move to a new neighborhood. The couple's union was frowned upon by many due to Masaki's status as an omega—a secondary gender that allows an individual to give birth. Even for an alpha—seen as the superior secondary gender—such as Hiromu, discrimination seems to be commonplace and a hindrance to a life of domestic bliss. Fortunately, the new family is not alone. Little Hikari becomes attached to Yuuki Hirai, the Fujiyoshis' lonely college student neighbor. Despite his initial reluctance, Yuuki ends up befriending the infant. Moreover, the family can also confide in Hiromu's childhood friend and coworker Tomohiro "Matsu" Matsuo. Although everything is going well for the young couple and their child, a sudden presence from the past might pose a problem for the peaceful life they dream of.

Three years into the war, Mahito Maki loses his mother in a tragic fire at the hospital. Shortly thereafter, his father marries Natsuko, the younger sister of Mahito's mother. They take Mahito out of Tokyo to seek refuge in his late mother's rural family home. There, Mahito is constantly taunted by a strange gray heron, who seems to have taken an interest in him. Unable to come to terms with his loss and struggling to adjust to a new life in an unfamiliar place, the boy is shocked to discover that Natsuko is pregnant. To make matters worse, the pesky heron can speak—and claims that Mahito's mother is still alive. Luring him into a mysterious tower near the residence, the heron says that Mahito can save her from death, but the boy is not easily swayed. When Natsuko disappears one day, however, Mahito watches her walk into the tower and becomes compelled to venture in to rescue her. He soon finds himself falling into another world below his, where life and death seem to be entwined. As he navigates through this foreign realm to find Natsuko, Mahito must understand what it means to live if he wants to safely return home.