A young Shirou Emiya and his adoptive father Kiritsugu Emiya travel to Fuyuki city to investigate the Sakatsuki family, rumored to harbor a child with extraordinary magical potential. They locate and rescue Miyu Sakatsuki from the ruins, and she is revealed to possess the power to grant wishes unconditionally. The storm that beset the city is tied to Miyu, suggesting her exposure to human thoughts and desires triggered the upheaval. Kiritsugu resolves to harness Miyu’s power to save humanity, but makes it clear to Shirou that Miyu should be treated as a tool rather than a person. Nevertheless, Shirou forms a quiet, growing bond with Miyu, even as Kiritsugu dies before he can learn how to wield her abilities.
Five years pass, and Shirou lives as a normal high school student, with Miyu as his adopted younger sister. They attend school alongside classmates Julian Ichigi and Sakura Matou. Shirou decides it is time for Miyu to see the wider world, and Miyu expresses a simple, hopeful wish: to see the ocean.
When Shirou begins to reveal his true motives for bringing Miyu outside, Julian Ichigi reappears to complete a ritual he had started. Shirou realizes Julian caused the vortex that swept through Fuyuki, and he tries to protect Miyu, only to be defeated by Julian and his follower Angelica, who leave him for dead while Miyu is kidnapped.
Shirou wakes under the care of a local priest, Kirei Kotomine. He explains that Julian is part of an ancient mage clan, the Ainsworths, who foresaw humanity’s end and seek the Holy Grail to avert it. Julian plans to use Miyu as a sacrifice to ignite the Fifth Grail War. In this peril, Shirou is helped by Sakura, who offers him a way to rescue Miyu but confesses that she would rather see him leave the city because of her feelings for him. The conflict intensifies when Sakura’s older brother Shinji attacks with the Assassin Card; Sakura is killed, and Shirou uses the Archer Card to empower himself and kill Shinji, who is revealed to be a puppet under Julian’s control.
With the Archer Card in hand, Shirou hunts the remaining Servant Card holders, only to discover they are all puppets of Julian. Kirei congratulates Shirou on “winning” the Fifth Grail War and directs him to an ancient cave where Miyu is being held. Shirou makes a fateful choice to use his wish to send Miyu to a different world where she can find happiness, even if that means defying Kiritsugu’s wishes.
As the ritual nears completion, Shirou confronts Angelica, the real holder of the Archer Card. Having used his Card to fuel the wish, he must fight Angelica with his own abilities. Though overpowered, Shirou buys enough time for the ritual to finish and Miyu is transported away. Miyu awakens in an alternate Fuyuki, now driven by a new objective: to locate the remaining magic cards and chart a path toward her own happiness.
