In Fuyuki City, a duel between two Servants destroys the entire area and engulfs it in flames. Ten years later, Shirō Emiya, The sole survivor of the destruction, devotes his life to following the ideal of his late adoptive father Kiritsugu: to become a hero of justice. In the present days, he helps out with tasks at his school and the local businesses freely with the aid of the magical powers taught to him by Kiritsugu, but is concerned about the sudden rise of violent crimes and lethal gas leaks in the city. At home, he is raised by his legal guardian Taiga Fujimura, with some assistance by his classmate Sakura Matō, who secretly has a crush on Shirō. While walking home one night, Shirō comes across the ruins left by the fire ten years ago and muses about a warning by Kiritsugu that if he saves one life, he will lose another. He then comes across a silver-haired girl who warns him to summon a Servant before abruptly vanishing. Meanwhile, another student at Shirō's school, Rin Tōsaka, summons an Archer-class Servant in preparation for the Fifth Holy Grail War and begins her search for magi with other Servants.

After having a dream about her father, who participated in and died during the previous Holy Grail War, Rin expresses her disappointment at not being able to summon a Saber-class Servant as she originally intended. She then asks Archer to reveal his real-life identity, although he is unable to recall his past. At school, Shirō learns from Ayako Mitsuzuri, head of the archery club, that Sakura's older brother Shinji has been acting more aggressively, presumably due to having his pride damaged after being rejected romantically by Rin. When he tries asking him about it, Shinji dodges the topic and later requests Shirō to clean the school's kyūdō dojo, which he accepts. The following night, while still at the school, Rin and Archer are confronted by a Lancer-class Servant, who engages Archer in battle. The duel is witnessed by Shirō, who is noticed by Lancer. Shirō tries to flee, but is caught by Lancer, who kills him before escaping. Moments later, Rin discovers Shirō's corpse and revives him with a magical jewel in a moment of pity, despite the Holy Grail War's rule that innocent witnesses must be killed. When Lancer comes back to kill him again at his home, Shirō accidentally summons Saber, the most powerful Servant. Upon spotting her, he becomes astounded by her beauty.

Saber refers to Shirō as her Master, which puzzles him, before she runs off to battle Lancer. She is wounded by Lancer's Noble Phantasm, from which she deduces his true identity, the ancient Irish hero Cú Chulainn. Lancer voices his disappointment at that before leaving, citing that his Master specifically ordered him to return. Shirō and Saber then introduce themselves to each other, though Shirō finds himself confused by Saber's strange terminology. Saber then attacks an approaching Rin and Archer, but is stopped by Shirō, though not before she badly injured Archer. After Rin discovers Shirō does not know even the most basic of spells, or the fact that he is a participant in the Holy Grail War, she takes him to a magus and her legal guardian, Kirei Kotomine, the overseer of the Fifth Holy Grail War. Shirō learns more about the Holy Grail War from him and decides to join it after learning the fire he survived ten years ago was a product of the previous war. Afterwards, Shirō, Saber, and Rin are confronted by the same silver-haired girl Shirō encountered earlier, who is accompanied by a massive Servant.

The girl introduces herself as Illyasviel von Einzbern, then has her Servant, identified as being of the Berserker class, attack Saber, who is still wounded from her battle with Lancer. Shirō and Rin are both helpless to stop Berserker, known in real life as the ancient Greek hero Heracles, from severely wounding Saber. Unable to see Saber suffer so grievously, Shirō eventually blocks a fatal blow intended for her. Puzzled by this, Illyasviel has Berserker de-materialize and leaves. As he dies, Shirō has a flashback to the night where Kiritsugu died, in which Kiritsugu confessed his wish to become a hero of justice and Shirō decided to take his place in accomplishing that wish. The next day, Shirō wakes up at his home to find that his body has miraculously healed itself, similar to Saber's self-regeneration ability. Later, he finds Saber at his dojo and starts to understand more about the type of person she is. As they walk back at the main home, Shirō begins contemplating about his feelings towards Saber.

Feeling guilty about how he has been making Saber hide away from plain view, Shirō decides to introduce her to Sakura and Taiga during dinner, saying she is a distant relative of Kiritsugu's. Feeling threatened by her presence, Taiga challenges Saber to a kendo duel, but winds up losing quickly and having to allow her to stay. Meanwhile, as they investigate the gas leaks occurring throughout the city, Archer asks Rin what she would do if she comes across Shirō, her sworn enemy, again, to which she replies she will kill him. After eating breakfast, Shirō heads for school alone, but not before Saber urges him to use a Command Seal to summon her if he ever thought he was in danger. At school, he learns Mitsuzuri had gone missing and that Shinji is suspected of having a connection to it. Afterwards, once school is out, Rin unexpectedly attacks Shirō, with the chase being witnessed by an unknown female Servant.

A fleeing Shirō is eventually cornered by Rin, who offers to spare his life if he gives her his Command Seals. However, he refuses, prompting Rin to try and kill him. Both are then distracted by a scream downstairs and he and Rin find an unconscious girl. As Rin attempts to heal her, a dagger flies through an open door, aimed for Rin, but Shirō blocks it with his arm, wounding himself in the process. He runs outside to find the female Servant, which is of the Rider class, and repels an attack by her. Shirō considers summoning Saber via Command Seal, but decides it is too risky to get her involved and resolves to confront Rider himself. Rider resumes her assault, and Shirō is nearly killed by her until Rin rescues him. At Rin's home, Shirō and Rin decide to form a temporary truce to find Rider's Master. Later on, Rin learns more about Shirō's magical training, which infuriates her, as Kiritsugu unconventionally prioritized fatherhood over the responsibilities of being a magus, something she found unforgivable. Shirō is later escorted home by Archer, who expresses his disapproval of Shirō's ideals and warns him that Saber will dislike not being able to fight because of Shirō's concern for her.

Saber confronts Shirō over not summoning her against Rider. Later on, she insists on accompanying him and Sakura to school. The exchange becomes even more tense when Rin stops by, lying that she and Shirō have agreed to walk each other to school, which causes Sakura to believe the two of them are dating and rush off in tears. Rin then successfully negotiates with Saber into allowing Shirō to walk with her alone. At school, after making up with Sakura, Shirō learns from Rin that Mitsuzuri was found alive, having been attacked by a Servant, presumed to be Rider. After discovering that Shirō can detect sigils related to a magical barrier placed over the entire school, Rin and Shirō set out to destroy most of them. Afterwards, the two bond over drinks and Shirō learns about Rin's late father. At the end of the day, after Rin leaves, Shirō feels the presence of an extremely large sigil and discovers it in the school dojo. He is then confronted by Rider and her Master, who is revealed to be Shinji.

Shinji defends his decision to set the barrier up over the school, explaining that it was a defensive measure against Rin. He also denies his involvement in Mitsuzuri's attack, and informs Shirō that the entire Matō family was once a clan of mages. Shinji then offers to form an alliance, stating that he too barely has any experience in using magic. Shirō turns down the offer and later informs Rin and Saber about a witch at the local shrine, Ryuudou Temple, who is also a Master, information that was given to him by Shinji. Saber insists they attack the Master directly and immediately, but Shirō and Rin believe it is more tactical to prioritize Illyasviel and Berserker over Rider and the Master at Ryuudou Temple. After this, Rin decides to officially move in with Shirō to make communications between them easier, which shocks Sakura and Taiga when they learn about it. Meanwhile, Shirō and Saber still cannot meet eye to eye regarding the strategy against the Master at Ryuudou Temple. Eventually, Saber decides to disobey Shirō's wishes and heads off for Ryuudou Temple alone.

Arriving at Ryuudou Temple, Saber battles an Assassin-class Servant claiming to be Sasaki Kojirō, who is guarding the temple gateway. Simultaneously, Rider breaches the temple's perimeter, but is attacked by skeletal beings called Golems and confronts their creator, a Caster-class Servant. Sensing the danger Saber is in, Shirō rushes to Ryuudou Temple on his own. After dodging Assassin's specialized attack, Saber uses whatever mana she has and prepares to use her Noble Phantasm, which gives Rider an opportunity to escape when she is outmatched by Caster. Saber's Noble Phantasm is then interrupted by an arriving Shirō, which prompts Assassin to leave and Saber to collapse from a lack of mana. Shirō then carries her back home, where she regains consciousness. When Saber criticizes Shirō for repeatedly protecting her and forcing her to not fight, Rin responds that it is because he simply does not want to see her hurt. As a result, Saber agrees to teach him how to fight with a sword.

Shirō has his first training session with Saber but fares poorly against her in battle. That same day, Shirō meets Illya in town and they converse in the park. After he returns home, Rin tells Shirō to swallow a jewel, which switches on his power to use magic.

Shirou is tricked to come to school by Shinji, and he finds himself in the midst of a trap after the Blood Fort Andromeda is activated by Rider. He manages to hold his own against Shinji, however, Shinji orders Rider to kill him. Rider's blade is unable to deal Shirō a killing blow, so she kicks him out of the window. With Shirō's death imminent, he summons Saber just in time. Saber fights Rider, and Shirō defeats Shinji, forcing him to call off Blood Fort. Rider uses her Noble Phantasm to escape from the school.

Shirō and Saber travel through town trying to find Shinji and Rider but are unsuccessful at first. When the fight between Saber and Rider commences, Saber is forced to unleash her Noble Phantasm, Excalibur, to defeat Rider, after her plan to defend to wait for an opportunity for Rider to be defenseless falls through when Shirō appears on the roof. Shirō carries Saber back after she collapses from using her Noble Phantasm.

Rin tells Shirō that he will have to use a command spell and make Saber assault humans in order to regain her mana. When Saber is sleeping, Shirō is shown a glimpse of her past, learning that she pulled Caliburn from the stone and became king of Britain. Archer tells Shirō that Saber knew using her Noble Phantasm would result in her disappearing and did not plan to do so but used it because she chose to protect him over everything else. While Saber is still weak, Shirō is captured by Illya, who gives him the proposition to become her servant, which he refuses. After Saber wakes up, she, Rin and Archer go looking for Shirō.

Illyasviel sets Berserker on them. Archer battles Berserker while Rin, Shirō and Saber get away. Archer manages to defeat Berserker once when he is battered by him to the hall. Illya is surprised when Archer calls her by her nickname, saying she is still as merciless. Archer knows that he will lose in the end but decides to deal as much damage as possible first, and uses his Noble Phantasm - Unlimited Blade Works, a reality marble. Archer manages to take five of Berserker's lives in total before he is ultimately defeated. Rin's last Command Spell disappears and Saber collapses in the forest.

In order to replenish Saber's mana, Shirō gives a part of his magical circuit to Saber, which means that he will never be able to use some sorcery or be on par with other magicians. After the transfer, Illya and Berserker come back for a final match.

After Shirō manages to trace a sword powerful enough to defeat Berserker - Caliburn, he and Saber work together to defeat him. Afterwards, Shirō takes Illya home with him.

With mass comas now occurring within the city, Shirō and the others decide to go after the Master and Servants at the Ryudōji shrine. After confirming that Sōichirō Kuzuki, one of Shirō's teachers, is Caster's Master, Sakura is taken captive by Caster to serve as a sacrifice in order to summon the Holy Grail.

Shirō, Rin and Saber attempt to rescue Sakura and to stop the Holy Grail from being summoned. While Saber fights Assassin, Shirō attempts to fend off Kuzuki, and Rin tries to save Sakura.

With victory all but won for Caster, an eighth Servant in golden armor appears and kills Caster and Kuzuki. After Shirō and the others escape, Saber reveals who this new Servant is and how she knows him.

While walking back home together, Shirō and Saber are attacked by the Servant Gilgamesh, who had previously saved them from Kuzuki and Caster. After Shirō traces a sheath for Excalibur, they manage to repel him. Later that night, Shirō makes his feelings clear to Saber and tells her that he wants her to stay with him after the war is over.

After going to Kirei's church, Shirō is captured and nearly killed by Kirei, but Saber comes in time and heals his wounds. Kirei orders Lancer and Gilgamesh to kill Shirō and Saber, but Lancer battles Gilgamesh in order to allow the two to escape. He is subsequently overwhelmed by Gilgamesh and slain.

After Illya is taken by Kirei, Shirō and Saber head to the Ryudōji shrine in order to defeat him. Saber fights with Gilgamesh while Shirō goes after Kirei.

By combining their powers, Shirō and Saber are able to defeat Gilgamesh and Kirei together. The final order Shirō commands to Saber is to destroy the Holy Grail. As Saber disappears, she admits her love for Shirō. An epilogue then takes place, with everyone returning to their normal lives, as if awakening from a long dream, and with Shirō satisfied with the life he has led forever remembering Saber and to enjoy a good life with Rin, Illya, Sakura and Taiga. Meanwhile, Saber has returned to her own time, where she tells Bedivere that she had a wonderful dream, and asks if one can relive dreams, to which Bedivere replies "of course". She then asks Bedivere to return Excalibur to the Lady of the Lake and, moments after Bedivere has accomplished her order, Saber peacefully dies under a tree.