A peculiar transfer student named Ougi Oshino has just arrived at Naoetsu Private High School. She is quickly introduced to senior student Koyomi Araragi by their mutual friend Kanbaru Suruga, in hopes of obtaining advice regarding a strange discovery she has made. After taking a look at the school's layout, Ougi notices that a classroom has appeared in an otherwise empty area—a place that should not exist. Unsure if this is the work of an apparition, Araragi and Ougi attempt to unravel the truth behind this enigma. But Araragi soon discovers, after finding himself locked in with Ougi, that the room holds the memory of an event he had long since forgotten.

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.

Since the death of his parents, Shinpei Ajiro had lived with the Kofune family and their two daughters—Mio and Ushio. Although he then left his home island to continue his education in Tokyo, Shinpei returns after Ushio tragically drowns during the attempted rescue of a little girl. During the funeral, his best friend informs him about bruises found around Ushio's neck, casting doubt over the cause of her death. Suspecting a murder has taken place, Shinpei reevaluates recent events, but strange incidents only continue to transpire. Disappearing people and other unexplainable occurrences lead Mio to recall an old folktale referring to entities called Shadows, which may not be entirely fantasy. Supposedly, an encounter with one's Shadow foretells the person's impending demise. Facing the dark side of Hitogashima Island, Shinpei stands against his grim fate to fulfill Ushio's final will—to protect Mio.

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.