Shirō returns home and reminisces about how Kiritsugu's ideals and the Fuyuki City fire ten years ago inspired him to become a hero of justice. Meanwhile, at Kirei's church, Caster visits a captive Saber, who is resisting her magical torture. She is then confronted by Kuzuki, who learns that her last two attacks had been done on her own free will and that she intends to use the church to obtain the Holy Grail's vessel. After waking up from a dream about Archer, Rin goes to Kirei's church with Archer and finds bloodstains. She concludes Caster attacked Kirei, but that he somehow managed to survive. The two then confront Caster and Kuzuki, but when Rin tries to battle them, Archer suddenly defends them from her attacks. Citing that Saber had been turned over to Caster's side, Archer pledges his allegiance to Caster, revealing that she is the ancient Greek princess Medea and allowing her to stab him with Rule Breaker, which takes Rin's Command Seals. Kuzuki then tries to kill Rin, but she is saved by a recovered Shirō. Caster tries to counter with Golems, but Archer stops her and has her release Shirō and Rin as a condition for him joining forces with her. While on their way back to Shirō's home, Rin confesses that Archer joined Caster because he knew Rin's strategies were hopelessly flawed, though Shirō counters this by telling her that even though she failed this time, it doesn't mean she was wrong. After comforting her, Shirō returns to her the jewel he found at her house, telling her that he had another one at his home. When Rin asks why he rescued her, Shirō confesses that he had feelings for her, which initially embarrasses her. However, she then thanks him for saving her life.

At his home, Shirō tells Rin that he plans on continuing to fight in the Holy Grail War, even without the use of a Servant. She replies that she has no choice but to let him before reaffirming their partnership. While discussing a strategy to defeat Caster and rescue Saber, the two decide to team up with Illyasviel, since Archer had told Rin that Berserker is in fact the ancient Greek hero Heracles, which might give them an advantage against Caster. Meanwhile, Caster recounts the time she was summoned by another magus for the Holy Grail War, only to be unsatisfied by his inefficient method of acquiring mana for her. After Caster requested to create mana herself, the magus realized he could not trust a magic user better than himself. As a result, he contacted Kirei and asked for another Servant, but Kirei told him to dispatch Caster first before making another Master-Servant pact. The magus then sent out a contract to Lancer's Master, a colleague, for Caster's death. In the meantime, she destroyed the magus's workshop, and then killed him when he returned and tried to use his Command Seals to force her into committing suicide. She was then gravely injured by Lancer and barely escaped with her life, but she was saved by Kuzuki, who became her new Master. In the present day, Illyasviel observes Shirō and Rin traveling to her villa, then sends out her maids to retrieve them. However, the villa is breached by Shinji and his new Servant, who reveals his knowledge that the Holy Grail's vessel is being held inside Illyasviel. When the maids retaliate in an effort to protect Illyasviel, the Servant kills them with a Noble Phantasm that summons numerous swords and fires them. He is then confronted by Illyasviel, who orders Berserker to attack him.

Ten years ago, in the aftermath of the Fourth Holy Grail War, Illyasviel had a vision of her mother Irisviel, who claimed her husband and Illyasviel's father, a participant in the war, betrayed them by refusing to accept the Holy Grail when it presented itself to him. At first, she refused to believe it, but realized the truth when her father did not return home. As time passed, she stumbled upon a room in her home, containing numerous homunculi that were created to serve Illyasviel's purpose, only to fail in their missions. Realizing she too is a homunculus from their dying messages, Illyasviel became disillusioned with her life. Later on, she met her current maids, who assisted her in summoning Berserker. However, she initially did not want it, resolving to participate and win the Holy Grail War by herself. During the final test of her Master-Servant link ritual, she became lost in the nearby woods, being separated from Berserker, and was mauled by a pack of wolves. Berserker rescued her, and afterwards, she realized it was protecting her out of its own free will. In the present day, Illyasviel and Berserker continue their battle against Shinji's Servant as Shirō and Rin arrive to witness the event. As the battle reaches the main entrance, the Servant eventually restrains Berserker using chains fired from his Noble Phantasm, allowing him to impale Berserker with a large spear. Then, he blinds and then stabs Illyasviel with a sword; as she crawls to Berserker's side, it makes one last attempt to strike the Servant, only to be killed. Shirō attempts to intervene, but Illyasviel dies in comfort, believing Berserker is still at her side.

As Shinji's Servant tears out Illyasviel's heart from her corpse, Shirō and Rin confront him and Shinji himself. When Rin threatens to kill Shinji, the two are forced to leave, but not before Shinji reveals his Servant's name as Gilgamesh. While burying Illyasviel, Rin confronts Shirō about his ideals and tells him that he needs to prioritize himself over others, otherwise he will break. He denies this and tells her about the time Kiritsugu rescued him, which caused him to admire him. However, Rin tells him that it is still wrong to value the lives of others over his own, citing that someone who was spared from a terrible tragedy has to live out their life to the fullest and that wishing for the happiness of others is no different from a machine. Despite her argument, Shirō remains committed to his ideals. Later on, as they evaluate Gilgamesh's power and conclude that Caster is still their priority, the two are approached by Lancer, who offers his assistance, which they accept. Meanwhile, Archer learns about Kuzuki's wish to help Caster succeed in her plan to return to her original era using the Holy Grail. Archer later confronts Shirō, Rin, and Lancer as they arrive at the church. Lancer engages Archer to give Shirō and Rin time to breach the church. As they do so, Rin informs Shirō that only one jewel (the same one he previously returned to her) exists in the world, and that Archer had already returned such a jewel to her.

Shirō and Rin confront Caster and Kuzuki, who engage them in battle. Meanwhile, Lancer overwhelms Archer with his attacks, after which Archer mocks his sense of loyalty and honor, thus infuriating him. As a result, Lancer tries to use his powerful Noble Phantasm to strike him down, but Archer is barely able to counter it with a magical barrier, which expends most of his strength in the process and destroys the church. After praising Lancer's power, Archer reveals he staged his betrayal of Rin so he could take advantage of Caster when she had her guard down, prompting Lancer to leave. Back at the church, Shirō and Rin are both overwhelmed by their opponents, but Archer suddenly appears and ambushes Kuzuki, firing several swords at his direction. Caster shields Kuzuki from the swords and is impaled herself. As she dies, she confesses to Kuzuki that her wish was already granted. Kuzuki then tries to fight Archer, explaining that since he had helped in disrupting the usual proceedings of the Holy Grail War, he had to finish what he started. He is then stabbed by Archer and crushed by a collapsing pillar. As Shirō attends to the captive Saber, Archer suddenly traps Rin inside a cage of swords and declares his intention, as a "Guardian", to kill Shirō.

Saber defends Shirō from Archer despite her chances of disappearing without a Master to anchor her down to the world, stating that she swore an oath to protect Shirō and that it remains unchanged. However, she is overwhelmed by Archer, forcing Shirō to intervene and take over in the fight. Rin takes advantage of Archer's distraction to form a Master-Servant pact with Saber, which she accepts, therefore making her Rin's new Servant. Fully restored, she subdues Archer, who mocks her for her wish of rectifying her legacy. He then casts Reality Marble, a spell that creates an alternate reality. Shirō, Rin, and Saber are subsequently transported to Unlimited Blade Works, Archer's Noble Phantasm, which is an alternate reality consisting of a barren wasteland filled with swords and levitating gears. Archer creates several duplicates of Saber's sword and fires them at her, but Shirō summons a sword of his own and destroys the duplicates, dissipating Unlimited Blade Works as a result. A weakened Archer grabs Rin, intending to use her as an insurance policy against Shirō and Saber while he recuperates. Before he flees, Shirō tells him to meet up with him at Illysaviel's villa. Later on, a restrained Rin wakes up after having another dream about Archer, and confronts him about his past as a Guardian. Then, Shinji and Gilgamesh arrive, and Archer agrees to give Rin to them for their own needs after he has finished killing Shirō. Back at his house, Shirō tells Saber to let him battle Archer while she rescues Rin, also implying that he knows of Archer's true identity. As they make their way to Illysaviel's villa, they are joined by Lancer, who is also determined to rescue Rin.

Shirō, Saber, and Lancer arrive at Illysaviel's villa, where they are met by Archer, who exposits on the true nature of his summoning: Rin had not in fact summoned him by chance, and the catalyst for his summoning was actually the pendent he carries, identical to the one Rin used to save Shirō. While Lancer runs off to retrieve Rin, Saber demands to know why Archer is so intent on killing Shirō. Archer responds that, like Shirō, he aspired to become a hero of justice and actually fulfilled that ideal, but became disillusioned by it and became a Servant so he could rectify it. He then forces Saber to reveal her back-story to Shirō: her true identity is that of King Arthur, who hoped to use the Holy Grail to undo her decision to become the king of Britain, as she believes it was her rule that eventually resulted in the country's destruction. When she then remarks that she and Archer are different in terms of how much they were able to live up to their ideals, Archer elaborates that when he became a Guardian in order to become a true hero of justice, he became disillusioned after he was forced to take lives in order to save many more. He eventually concluded that his ideals were shallow and that it was impossible to save everyone, just as he envisioned. Archer then reveals his true identity: Shirō's future self, the Heroic Spirit Emiya. Meanwhile, Shinji tries to rape Rin, only for Lancer to arrive and incapacitate him. Then, Kirei suddenly appears, exposes himself as Lancer's Master, and reveals he was the one who killed Rin's father in the previous Holy Grail War. He then orders Lancer to kill Rin, intending to use her body as a vessel for the Holy Grail. When Lancer refuses, Kirei uses one of his many Command Seals and orders him to commit suicide, which he does. Back at the main entrance, Emiya tosses Shirō one of his swords and orders him to kill himself with it. However, Shirō refuses, proclaiming that since he learned Emiya's story, he will do all he can

hirō and Emiya begin their battle, with Shirō finding that while he is only barely able to hold off Emiya's attacks, he is slowly becoming stronger the longer he clashes with Emiya. Meanwhile, Kirei prepares to take Rin's heart against Shinji's protests. However, Lancer, mortally wounded but still alive, fatally stabs Kirei. Shinji, on the verge of insanity, takes this opportunity to try and rape Rin again, only to be chased off by Lancer, who lightly wounds him. After freeing Rin, he collapses to the ground and laments how he would have liked for Rin to be his Master. Both Rin and Lancer bid farewell to each other, and as Rin leaves, Lancer sets a fire to destroy both him and Kirei's corpse. Back at the main entrance, Shirō and Emiya continue to battle, with Emiya activating Unlimited Blade Works and slowly gaining the upper hand. As their swords clash, Shirō begins to see Emiya's memories and becomes aware of what his future holds in store for him. With his belief shaken, Shirō is quickly defeated by Emiya and left on the verge of death. As he lies on the ground, Shirō begins to reflect on the memories he gained from Emiya, as well as the memories of Kiritsugu saving him ten years ago. From this, Shirō concludes his ideals are not wrong, and he decides to continue to fight. At that moment, Saber's scabbard Avalon, which Kiritsugu had placed inside Shirō to restore the injuries he sustained from the fire, activates and heals Shirō's wounds. With his confidence in his ideals restored, Shirō prepares to battle Emiya again, with the declaration that he will defeat him.

Shirō and Emiya continue their battle, with Emiya chastising Shirō for continuing to pursue his ideal and declaring that he will remove every trace of him in existence. However, as the battle continues, Emiya begins to realize that Shirō, being himself, will never give up and that it is pointless to defeat him now. Finally, as he explains the beauty he saw in his ideal, Shirō's spirit begins to overwhelm Unlimited Blade Works, and he rushes Emiya. Emiya tries to react, but he becomes distracted by a flashback of Kiritsugu's last moments and is wounded by Shirō, just as Rin arrives. With this, Emiya admits defeat and allows Shirō, Rin, and Saber to escape, before being impaled by three swords fired from Gilgamesh's Noble Phantasm. Declaring his hatred for fakes, Gilgamesh fires more swords at Shirō and Emiya, but Emiya pushes Shirō out of the way and dies after taking the full blow of the attack. Saber, expressing a familiarity with Gilgamesh, demands to know why he is here, and he explains that after the end of the Fourth Holy Grail War, in which he was an Archer-class Servant, he bathed in the Holy Grail during its destruction at the hands of Saber, also a Servant in that war, and took physical form. He then explains the Holy Grail's true function as a container for thousands of curses, before announcing his intention to take it for himself and use it as a weapon to eradicate the human race, being disgusted by the lifestyle of modern humans and hoping to rule over any potential survivors. He then leaves the villa and later finds Shinji in the forest, learning from him about Kirei's death and the reason behind Rin's escape. When Shinji asks about finding a vessel for the Holy Grail, Gilgamesh implants Illyasviel's heart into him, deeming him a worthy enough vessel, and leaves him as he begins to mutate into a massive, shapeless form of flesh.

Returning to Shirō's home, he, Rin, and Saber all decide to avenge Emiya and stop Gilgamesh by destroying the Holy Grail once and for all. Through the use of familiar spirits, Rin deduces that the Holy Grail is being summoned at Ryuudou Temple. She then explains that Shinji, the only other magus participating in the Holy Grail War, would be the only viable candidate as a substitute vessel, as it was apparent Illysaviel was supposed to turn into the Lesser Grail at the end of the war. While devising a strategy to defeat Gilgamesh, Rin realizes Emiya was the only one who could perfectly counter him, since he had the ability to summon a duplicate of any kind of weapon. She then concludes that Shirō needs to master Unlimited Blade Works so he too could be an even match against Gilgamesh. Since he doesn't have the sufficient mana to do so, Rin improvises, performing a ritual that implants her Magic Crest into Shirō, thus allowing them to share their mana storage. During the ritual, Shirō inadvertently taps into Rin's memories, something that embarrasses Rin when she finds out. Afterwards, Shirō finds Saber exploring his house, and she thanks him for showing her the way to her dream. Then, she has him promise that he and Rin will survive the Holy Grail War. Meanwhile, Gilgamesh has finished transporting Shinji to Ryuudou Temple, which summons the Holy Grail.

Shirō and Rin plan to breach Ryuudou Temple and rescue Shinji while Saber fights Gilgamesh and destroys the Holy Grail. Saber reveals she can only use her Noble Phantasm, Excalibur, once before fading, since Rin cannot supply her with enough mana due to her sharing it with Shirō. At Ryuudou Temple, Shirō and Rin observe Shinji's mutated form and a torrent of black ooze pouring out from the Holy Grail, pooling around Shinji and forming a lake. They are then confronted by Gilgamesh, who elaborates on his intentions and explains that there are too many people in the modern era than there are significance and purpose. At the main gate, Saber instead comes across Assassin, who is still guarding the temple despite Caster's death, as it is his anchor to the world. He reveals that he is not actually the fictitious Sasaki Kojirō, but a nameless swordsman similar to him, then expresses a desire to finish his duel with Saber before he fades. As Shirō duels Gilgamesh, the Holy Grail is bombarded by what Gilgamesh claims to be mankind's malevolent wishes. Rin approaches the mass of flesh and manages to remove Shinji from it, causing it to try and use Gilgamesh as a replacement vessel. However, he defends himself with a powerful sword called Ea. Meanwhile, as they duel, Assassin reveals to Saber he is already starting to fade and tries to use his Noble Phantasm, but Saber fatally wounds him.

Having defeated Shirō, Gilgamesh mocks his ideals; he agrees with him, but reaffirms his dream nevertheless. As Gilgamesh attempts to finish Shirō off, Saber arrives and shields him, but is ordered by Shirō to save Rin. Having an epiphany about the true nature of his powers, Shirō activates Unlimited Blade Works and uses its infinite number of replicate swords to counter Gilgamesh's Noble Phantasm. Meanwhile, Saber approaches the Holy Grail and recognizes it as a corrupted, improperly-summoned Servant called Angra Mainyu. She locates Rin, who uses two Command Seals and orders her to destroy the Grail with Excalibur as she is being consumed by Angra Mainyu. When Rin loses hope at surviving, Emiya's voice chides her for giving up and a barrage of swords pelts Angra Mainyu, freeing her. With Rin free and using her final Command Seal to augment her attack, Saber unleashes Excalibur and destroys Angra Mainyu's manifestation and the Holy Grail. As she fades, Saber laments that she will be unable to watch over Rin and Shirō, but accepts that her role is over. Inside Unlimited Blade Works, Shirō manages to overwhelm Gilgamesh, who angrily tries to draw Ea, but Shirō cuts off his arm and slashes him across the chest before running out of mana. Gilgamesh tries to finish him off, but a portal to the Holy Grail opens and engulfs him. He ensnares Shirō with a chain in order to pull himself out, but Emiya, having survived Gilgamesh's attack, intervenes by shooting a dagger into Gilgamesh's head, fatally wounding him. As he speaks his last words, Gilgamesh is consumed by Angra Mainyu before the portal closes. Rin and Emiya say goodbye as he fades away, with Emiya asking her to look after his past self. Shirō reunites with Rin, and they walk off together.

Two years after the events of the Fifth Holy Grail War, Shirō and Rin are living together in an apartment in London while they both study under the Mages Association at the Clock Tower, with Shirō being Rin's apprentice as protection for her. However, he is still struggling with following his ideals without following the same path as Emiya. One day, Rin has a duel with fellow classmate and neighbor Luvia Edelfelt, who repeatedly flirts with Shirō, and loses, much to her chagrin. Afterwards, she and Shirō talk about his invitation to officially join the Mages Association, which conflicts with his ideals. One morning, Rin decides to take Shirō to Glastonbury, the final resting place of King Arthur, so he could say goodbye to Saber. During the trip back home, Shirō reminisces about his graduation from his second year of high school. The next day, Shirō encounters Waver Velvet, a survivor of the Fourth Holy Grail War, who questions him about his reasons for coming to the Clock Tower and studying magic after surviving the Holy Grail War. Shirō says he knows it to be stupid, but he wants to dedicate his life to fulfilling his ideal. Waver responds that while his desire is indeed idiotic, it is not something to be laughed at. Later, Shirō returns to the apartment and informs Rin he has turned down the invitation, saying he cannot change who he is, even if he is destined to meet the same fate as Emiya. Rin responds that the difference between him and Emiya will be how far he goes in following his ideals. She then assures him that she will always be by his side. In the epilogue, Emiya is shown sitting in Unlimited Blade Works, reconsidering his life and purpose. While he admits his regrets and a belief that Shirō will end up cursing the path he himself took, he asserts in the end that he was not wrong in his ideals.