Fifteen years ago, disaster struck human civilization, and now dangerous man-eating monsters roam the ravaged lands, posing an existential threat to the remaining survivors. Amid this turmoil, an isolated facility shelters children and nurtures them in peace. However, as a few among them find out about the world beyond the narrow periphery of their nursery's walls, their curiosity about it slowly grows. Meanwhile, in the outside world, young survivors Maru and Kiruko band together to search for a special place called Heaven, each for their own reasons. Carrying past burdens and tragic secrets, the two hope to find answers to the cruelty they have experienced in their lives and in the world, which still remains in tatters.

Kazuya Kujou is a foreign student at Saint Marguerite Academy, a luxurious boarding school in the Southern European country of Sauville. Originally from Japan, his jet-black hair and dark brown eyes cause his peers to shun him and give him the nickname Black Reaper, based on a popular urban legend about the traveler who brings death in the spring. On a day like any other, Kujou visits the school's extravagant library in search of ghost stories. However, his focus soon changes as he becomes curious about a golden strand of hair on the stairs. The steps lead him to a large garden and a beautiful doll-like girl known as Victorique de Blois, whose complex and imaginative foresight allows her to predict their futures, now intertwined. With more mysteries quickly developing—including the appearance of a ghost ship and an alchemist with the power of transmutation—Victorique and Kujou, bound by fate and their unique skills, have no choice but to rely on each other.

The Fifth Holy Grail War continues, and the ensuing chaos results in higher stakes for all participants. Shirou Emiya continues to participate in the war, aspiring to be a hero of justice who saves everyone. He sets out in search of the truth behind a mysterious dark shadow and its murder spree, determined to defeat it. Meanwhile, Shinji Matou sets his own plans into motion, threatening Shirou through his sister Sakura Matou. Shirou and Rin Toosaka battle Shinji, hoping to relieve Sakura from the abuses of her brother. But the ugly truth of the Matou siblings begins to surface, and many dark secrets are exposed. Fate/stay night Movie: Heaven's Feel - II. Lost Butterfly continues to focus on the remaining Masters and Servants as they fight each other in the hopes of obtaining the Holy Grail. However, as darkness arises within Fuyuki City, even the state of their sacred war could be in danger.

After surviving the brutal challenges of Idofront, Riko now possesses a White Whistle, allowing her to descend into the Abyss's sixth layer—The Capital of the Unreturned. Alongside Reg and Nanachi, Riko begins to explore the uncharted domain, where the ruins of the promised Golden City are located. As the trio starts to adapt to the harsh environment, they soon encounter dangerous creatures and treacherous landscapes. Their expedition leads them to a village inhabited by strange beings known as hollows. Despite the creeping sense of unease that welcomes them, the three venture onward to uncover the mysteries of the settlement and long-lost legacies of the forgotten adventurers who once descended into the horrors of the unexplored Abyss.