The events of the previous episode unfold from a different perspective, as Shirō wards off Lancer's attacks before summoning his own servant, Saber.

Back in Shirō's home, Rin explains that he had been chosen as a Master for the Holy Grail War, then explains the basics behind it. When Shirō is unable to comprehend the situation, Rin decides to take him to see Kirei Kotomine, a priest who is her legal guardian and also the overseer of the Holy Grail War. When they arrive at Kirei's church and meet up with him, Shirō learns that once someone is chosen to fight as a Master, their responsibilities are unavoidable. He then learns about the Holy Grail and the purpose of the Holy Grail War. Then, Shirō learns that there were four Holy Grail Wars before the current one, with the latest one taking place ten years ago. When he asks what happens if a Master with dark intentions wins the Grail, Kirei replies that there can be no action taken against the victor, and that the only way he could prevent such a Master from winning is to win it himself. He then adds that at the conclusion of the previous Holy Grail War, a Master with dark intentions touched the Grail, resulting in the fire that Shirō survived, a revelation which horrifies Shirō. Kirei then reveals that before the unworthy Master appeared, another Master actually won the Grail and held it, but because the Grail hadn't fully materialized at the time due to this Master refusing to fight, it deemed him unworthy to hold it. As a result of all the information he had just learned, Shirō finally accepts his responsibilities as a Master. Regrouping with Saber outside of the church, Shirō declares that he will be her Master, and they agree to fight in the Holy Grail War together. Later, Archer informs Rin that since Shirō is now a proper Master, they should attack, but she responds that she still has a debt to pay him and instead decides to let him and Saber return home. Moments later, they are confronted by the same silver-haired girl Shirō briefly met earlier, who is revealed to also be a Master, and her Servant, which Rin identifies as belonging to the Berserke

The girl introduces herself as Illyasviel von Einzbern, a name which Rin recognizes. She and Archer evaluate Berserker's strength before Archer moves to a farther position so he could attack Berserker from a distance. Berserker then attacks Saber, who is overwhelmed by his brute strength and agility. Archer and Rin try to provide support for Saber, but Berserker constantly winds up being unaffected by their strikes. When the fight moves away into the suburbs, Rin orders Shirō to run, but he remembers his agreement with Saber and instead follows them. As the fight progresses, Kirei is visited by a mysterious blond, red-eyed man, and they both claim their intentions to witnessing the Holy Grail's materialization in its fullest detail. The fight then moves through a forest and into a local cemetery, while Rin tries to kill Illyasviel, but she counters with several bird-shaped homunculi. Rin is rescued by Archer's attacks. While running back to Saber, Rin runs into Shirō, and they watch as Saber kills Berserker, which then suddenly resurrects and regenerates itself, one of its Noble Phantasms. Archer projects and fires a sword-shaped arrow at Berserker, which engulfs it in a massive explosion, but it fails to affect it. Illyasviel, impressed by Archer's strength, withdraws Berserker and flees. Seconds later, Shirō suddenly begins vomiting blood.

Shirō wakes up in his home, uninjured and Rin sitting at his side. She leaves, but not before telling him that when they meet next time, it will be as enemies. Shirō then finds Saber in the dojo, and she reveals that he has self-healing magical capabilities, explaining the absence of the injuries he sustained in the battle with Berserker. Saber then explains the mechanics of the seven Servants and the advantages and disadvantages of knowing a Servant's real-life identity, then asks that she not reveal her identity to him since he is an inexperienced mage, a request he approves of. Shirō and Saber then go to school to deliver lunch to the archery club. There, Saber explores the school and has a tense encounter with Sōichirō Kuzuki, one of the instructors, before they are interrupted by Shirō. Later that day, while still at the school, Shirō is approached by Mitsuzuri, who asks if he will rejoin the archery club before noting he has never smiled in his life. While walking home with Saber, Sakura, and Taiga, he explains that Saber is a friend of Kiritsugu's and will be staying with him temporarily. Sakura is seemingly horrified by the idea, but Taiga approves under the condition that she stay in the home as well during that time. Elsewhere, Rin and Archer investigate an office building purportedly having a gas leak and find it is actually the work of another Servant who is absorbing the life force of the employees inside. They theorize that the Servant responsible is of the Caster class and is likely at Ryuudou Temple. When Rin decides to pursue Caster, Archer notes that she is ignoring Shirō, who she could easily kill to get him out of her way, and asks what will happen if Shirō approaches her again.

Five years ago, Kiritsugu tells Shirō about how he once wished to become a hero of justice. Shirō promises him that he will fulfill that dream for him, after which Kiritsugu passes away in satisfaction. In the present day, Shirō goes to school alone, despite Saber's insistence that she accompany him. At school, he learns from Issei that Mitsuzuri had gone missing the previous day and that she was last seen arguing with Shinji, who is currently absent, with no one able to contact him. As school ends for the day, Shirō is confronted by Rin, who attacks him despite his protests. After a brief chase, Rin eventually corners him and tries threatening him into handing over his remaining Command Seals, but before she could carry out her threat, they hear a scream. Shirō investigates and finds an unconscious student who had most of her mana absorbed. As Rin treats the student, Shirō is wounded after shielding her from an incoming attack by an unknown female Servant. He then pursues the Servant into the nearby woods, where he is restrained and nearly killed by her, only to be saved by Rin, whose appearance prompts the Servant to flee. Rin treats Shirō's wounds and decides to call off their fight, taking him to her house to evaluate the situation. Then, the two agree to have a truce and track down the Servant and her Master together. The following night, Rin learns of Shirō's magical training, which she is outraged by, as Kiritsugu didn't adhere to the tradition of magecraft by prioritizing himself as a father rather than a mage.

While walking back home, Shirō senses Archer following him. After a brief conversation, Archer responds that he doesn't have any interest for the Holy Grail. He then explains that Servants are no more than mere tools for their Masters and reveals that he died with no unfulfilled dreams before disappearing. Returning home, Shirō learns from Taiga that Mitsuzuri was found alive without any visible injuries. He then meets up with Saber and tells her of the truce he made with Rin, which she approves of. The next day, at the school library, Shirō and Rin discuss on how to locate the female Servant's Master before Shirō senses a sigil in one of the bookshelves, which Rin disables. They then explore the school grounds and disable other sigils, which they realize were set up for strengthening the magical barrier placed over the school. While preparing to head home, Shirō is confronted by Shinji, who reveals himself as the female Servant's Master and also the one who set up the barrier, also exposing the entire Matō family as a former clan of mages. Shinji then tries to convince Shirō to form an alliance, but he turns the offer down, although he promises to keep quiet about their conversation. The following night, Shirō wakes up and finds himself restrained at Ryuudou Temple. He is approached by a hooded female Servant, identified as Caster, who admits responsibility for a purported series of gas leaks all over Fuyuki, enraging Shirō. Caster then expresses her intention to remove Shirō's Command Seals and transplant them to her own Master, but before she could do so, Archer intervenes and prepares to engage Caster in battle. Meanwhile, Saber senses Shirō's disappearance and heads to Ryuudou Temple, only to be faced by a second Servant, who identifies himself as an Assassin-class Servant and claims to be the Japanese swordsman Sasaki Kojirō. Then, he challenges Saber to a duel.

Saber engages Assassin in battle after he threatens the safety of Shirō, and is shocked to find that despite her advantages in strength and agility, she cannot break through his defenses. At Ryuudou Temple, Caster reveals that Assassin is her own Servant, as she is a mage as well. Archer claims that she broke the rules of the Holy Grail War and insults her tactics before engaging her in battle. After a while, Archer manages to critically wound Caster, prompting Assassin to finish his assault prematurely with his Noble Phantasm. When Caster asks Archer why he is not finishing her off, he responds that his main goal was Shirō's safety and he is not a believer in senseless slaughter. This causes Caster to compare Shirō and Archer, claiming that their ideals are so identical that they are "the same", before trying to ask them to join her, although both reject the offer. Archer then allows Caster to flee despite the fact that she will continue to kill innocent people. When Shirō protests this decision, Archer counters that doing so will be instrumental in the defeats of not only her, but those of her Master and Berserker. Disgusted by Archer's willingness to allow collateral damage, Shirō criticizes his ideals, and Archer defends them, citing that if Caster were to win the Holy Grail, the damage would extend far beyond Fuyuki. Unable to accept this, Shirō tries going after Caster alone, but is slashed in the back by Archer. He staggers out of Ryuudou Temple and is tended to by Saber, who survived Assassin's Noble Phantasm. Archer continues his assault, but is distracted by Assassin, who is impressed by Saber's power and allows her and Shirō to escape. At the dojo, after commenting on Archer's swordsmanship, Shirō, now unwilling to lose to him again, asks Saber to teach him how to fight with a sword.

After having a lesson with Saber on how to use a sword, Shirō notices that he performed better than during his previous lesson. He notes to Saber that he is using Archer's techniques as a basis for his study, which seems to upset Saber. Arriving at school late, Shirō is met by Shinji, who greets him ominously. During lunchtime, Rin reluctantly forces Shirō to eat with her at the school rooftop. She reveals that she learned about Archer's attack on him and was forced to use a Command Seal to prevent him from further attacking him. Shirō asks about the Matō family being a bloodline of mages; Rin responds that while they are, their magical abilities died off with each generation. She then admits that she had recently found out Shinji was a Master, but relented in attacking him because he lacked experience in magic, and that as a result, there is another Master present in the school. Then, Shinji's Servant activates a second, much stronger magical barrier around the school, which absorbs the mana of everyone but Shirō and Rin. The two are attacked by skeletal beings called Golems, and Shirō summons Saber via Command Seal. Saber battles the Golems while he and Rin go to the school's first floor to disable the barrier. After dispatching several Golems, Saber faces off against Shinji's Servant, who is identified as being of the Rider class, and manages to stab her, but Rider is revealed to be an apparition created by Caster, who disappears. Meanwhile, Shirō and Rin find Shinji and the corpse of the real Rider, which dissolves, causing the barrier to dissipate. Shinji refuses to identify the Servant who killed Rider and flees the school. After Shirō, Rin, and Saber assess the situation and deduce that Caster killed Rider, Rin notes Shirō's ability to recognize the conditions of the unconscious students and employees, and he replies that he was used to seeing dead bodies, which confuses Rin.

Following the events at the school, Shirō allows Saber to sleep next to his room so she could prevent him from being taken by Caster again. Meanwhile, Shinji arrives at Kirei's church and pleads with him to offer him shelter and protection. However, when he finds out he was the first Master to lose his Servant, he blames the loss on Rider, yelling that she was useless as a Servant. Realizing Shinji still has a resolve to fight, Kirei tells him there is one additional Servant available for usage. After clearing Issei of being Caster's Master, Shirō encounters Rin, who is spying on the blond-haired, red-eyed man who visited Kirei at his church; the man had been observing the Matō home for some time. When the man leaves, Rin asks Shirō about what would happen if someone were to be adopted by another family against his or her will, and forced to grow up in their care. While eating dinner, Taiga tells Saber about Shirō's childhood and Kiritsugu, commenting that they seemed to be polar opposites of each other due to their personalities, and also mentions Shirō's wish to become a hero of justice. When Saber asks him why he wanted to become a hero of justice, Shirō vaguely replies that it was because he looked up to them. However, while in his room alone, he concludes he only wanted to follow in Kiritsugu's footsteps, and then remembers Archer's words that his ideals were flawed.

Rin wakes up after having a dream about how Archer became a Servant in the first place. She later discusses Shirō's reliability as an ally with Archer, who suggests Caster would be a more efficient partner for them, which upsets her. At school, Shirō notices Issei talking with Kuzuki and learns from him that Kuzuki lives at Ryuudou Temple with a mysterious woman who is believed to be his fiancée. Rin theorizes from the information that Kuzuki is Caster's Master and plans on confirming them by attacking Kuzuki with a non-lethal magical attack and observe his reaction. The following night, Shirō, Rin, and Saber set up their quarters at an abandoned gas station where Kuzuki usually passes by. When he arrives, Rin fires the magical attack on him, but he is unaffected and Caster arrives for assistance. An outraged Shirō confronts Kuzuki and asks if he knew about Caster's attacks on innocent people; Kuzuki responds that he was unaware but did not care the slightest, revealing himself to be a former killer. Rin then attacks Caster as a distraction while Saber tries to strike Kuzuki, but Kuzuki uses magically-strengthened fists to subdue Saber and Rin, then brutalizes Shirō. In response, he summons Archer's dual swords and uses them to repel Kuzuki's attacks. When Saber and Rin regain consciousness, Kuzuki and Caster flee. Rin asks Shirō how he was able to summon weapons, and he reveals that while he specialized in strengthening magic, he first succeeded at using projection magic. Meanwhile, Shinji meets his new Servant, the blond-haired, red-eyed man, who dismisses his strategy to kill innocent people for their mana and reveals his plan to use the Holy Grail to kill most of the human population in the world.

After the battle with Caster and Kuzuki, Shirō and Saber return home. Shirō claims he is fine so as not to worry Saber, but is clearly in pain and off-balance as a result of using projection magic. The next day, he goes to school and finds that Kuzuki is absent due to what is claimed to be an illness. After school, Shirō returns home, where Rin suddenly arrives unannounced. The two proceed to formulate a strategy to deal with Caster. However, their only viable plan is a full-frontal attack against Ryuudou Temple. While Rin and Saber agree it is their best shot, they fear that Caster might opt to destroy the entire temple if she is cornered. After dinner, Shirō meets Rin in the courtyard, where she muses that Shirō's house is more open and welcoming than her own, and that perhaps it is better that Shirō did not adopt the lifestyle of a true mage. She then tells Shirō that she became a mage because she personally enjoys studying magic, and asks him what his reasons for studying magic are. Shirō responds that he wants to use magic to help others, which frustrates Rin, who cites that it is not right for him to put the happiness of others above his own. She then tells Shirō that she will be staying at his house for the night. Later that night, Shirō returns to the shed to practice his magic. Saber comes in to check on him, and he tells her how Kiritsugu was a good man and how he wanted to be a hero like him. Archer then arrives and asks Shirō about his symptoms, knowing precisely the side-effects of using projection magic. He tells Shirō that the pain he is feeling is due to activating magic circuits that had long lay dormant. After repairing Shirō's magic circuits and noting that he once went through a similar experience, Archer warns him that his ideals are meaningless and doomed to fail, something Shirō denies.

While returning home from a trip in the next town, Shirō, Rin, and Saber find themselves inside a magical barrier, and they are ambushed by Caster and several water Golems. Caster reveals she has taken Taiga hostage and threatens to kill her unless Shirō hands over his magical circuits to her. When Shirō refuses, Caster tells him that she knows about the fire that he survived ten years ago, then claims her knowledge of a method to summon the Holy Grail without any further fighting, which can only be accomplished by Saber's mana. Shirō allows Caster to take his Command Seals in order to rescue Taiga, but an ambivalent Saber engages Caster in battle. Shirō uses a Command Seal to stop Saber, allowing Caster to stab her in the heart with a dagger-like Noble Phantasm called "Rule Breaker", which takes Shirō's remaining Command Seals and gives Caster control over Saber. After releasing Taiga, Caster forces Saber to kill Rin, but Shirō is injured while taking the blow. Saber then resists against Caster's magic long enough for Shirō, Rin, and Taiga to escape with assistance from Archer. Regaining consciousness at Rin's house, Shirō finds a jewel. He recognizes it as the same one that had been used on him while Rin revived him after he was stabbed by Lancer during the first battle. Meanwhile, Caster arrives at Kirei's church and demands the location of the Lesser Grail, the vessel for the Holy Grail. When he refuses to disclose it, she has him attacked by Golems. Shirō finds Rin at the top of a skyscraper and tries offering his assistance. However, she tells him that without Saber as his Servant, there is no longer a reason for him to be involved in the Holy Grail War and leaves with Archer. As she leaves, Rin warns him to stay out of the war, otherwise he will die.

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.