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.