Years ago, a young Kiritsugu lived on Alimango island in the Philippines with his father Noritaka and his father's assistant, a local girl named Shirley who called him Kerry. Noritaka was conducting research on immortality using plants. Despite being told by the townsfolk to stay away from Noritaka, Shirley is convinced his research will help the world and tells Kiritsugu she hopes he grows up to be great man. But one morning, Kiritsugu's father asks him if he went into his lab, and then tells him not to leave their house. Kiritsugu ignores his father's warning and goes to search for Shirley, only to find her at her house in a frenzy, devouring live chickens. Shirley reveals that she went into Noritaka's lab and use his immortality formula on herself, which turned her into a Dead Apostle vampire with an incessant craving for blood. Shirley begs Kiritsugu to kill her while she is still herself, but he is unable to do it, and she attacks the townsfolk, turning them into Ghouls. As chaos spread across the island, Church Executors and Mages from the Mages Association arrive to stop the outbreak and cover up the incident. Kiritsugu is saved from the Ghouls by a mercenary named Natalia Kaminski. She explains she is there to eliminate the magus responsible for the outbreak, which Kiritsugu realizes is his father. He confronts Noritaka over his work and its consequences, but his father simply shrugs them off as an accident, and tells Kiritsugu he plans to continue his experiments elsewhere. Angered at his father's response, Kiritsugu kills him. Emotionally broken and with nowhere to go, Kiritsugu agrees to escape together with Natalia.

Kiritsugu visits an ailing Iri in the storehouse. She gives her husband the scabbard Avalon and asks him to bring their daughter Ilya to see Japan once the War is over. Learning from Maiya that Saber has gone to battle Rider, Kiritsugu assigns Maiya to protect his wife while he goes to assassinate Tokiomi. Meanwhile, Waver heads to the forest where he summoned Rider in order to replenish his mana before Rider's intended fight with Saber, whom he wishes to battle to set her straight on what it means to be a king. Kariya has a nightmare in which Berserker speaks to him before awakening chained in the cellar of the Matou house. To heal Kariya, Zouken forces him to swallow the crest worm that first tasted Sakura's purity. Iri talks with Maiya about the latter's past as a child soldier, and implores her to live her own life after the war. Iri tells Maiya her wish that this Grail War will be the last so that Ilya can live a normal life. At the same time, Kiritsugu arrives at the Thosaka mansion only to discover that Tokiomi is dead. In the interval, Rider attacks Iri and Maiya. Kiritsugu uses a Command Seal to order Saber to return to the storehouse, where she finds Maiya injured and Iri abducted by Rider; she gives chase on her motorcycle. On reaching the storehouse, Kiritsugu finds the dying Maiya, and comforts her in her last moments through his own tears.