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.

As a young boy, Prince Oscar Lyeth Increatos Loz Farsas was cursed by the Witch of Silence, rendering it all but impossible for any woman to bear him a child. After 15 years of fruitlessly seeking a way to lift the spell, Oscar resorts to enlisting the help of a different witch. To this end, he heads to the Azure Tower, home of the Witch of the Azure Moon. Ascending the tower is no easy task; for decades, no one has overcome the array of traps, puzzles, and enemies designed to repulse any challengers. Oscar, however, easily climbs to the top, where he meets the fabled witch, Tinasha. To the prince's surprise, despite being hundreds of years old, Tinasha looks like a beautiful young woman in her late teens. Oscar explains his circumstances to the witch, who quickly perceives the true nature of his affliction. Though she claims that undoing the spell would be tremendously difficult, Tinasha proposes a workaround—to find Oscar a partner capable of withstanding the curse's effects. Realizing that such a woman is right in front of his eyes, Oscar boldly tells the witch to marry him. Though he is promptly rejected, the young prince refuses to back down, and the two eventually reach an agreement: Tinasha will leave the tower and live with Oscar for the next year. As the two continue searching for a way to lift Oscar's curse, word of Tinasha's emergence from isolation spreads, catching the attention of all sorts of old acquaintances.

Shidou Itsuka faces greater peril than ever due to his continued involvement with Ratatoskr. He has already sealed 10 Spirits, and Isaac Westcott, leader of Deus Ex Machina Industries, has finally decided to kill Shidou and plunder the Spirits' powers for himself. To achieve his goal, Isaac declares an all-out war against Ratatoskr, forcing the organization to exhaust its resources to ensure Shidou's survival. Despite being severely outnumbered and outmatched, a glimmer of hope exists in the form of the Spirit of Time, Kurumi Tokisaki. Shidou must seal and acquire Kurumi's power to travel to the past and confront the Spirit of Origin—the catalyst that started it all.

Percival has always lived with his grandfather on God's Finger, a remote haven that sits high above the clouds. And though he loves the simple life, he secretly longs for adventure. But Percival's life is changed forever when an intruder—who shares a shocking connection with him—tears away everything he's ever known. With nothing left to do but chase down the one who took everything from him, Percival sets out on his own. During his journey, the sheltered boy discovers that there are a lot of things he doesn't know about normal life. Luckily, he meets friends along the way who can help him get by—but how will they react when they find out about Percival's destiny... and how it's connected to the end of the world?