Ten years ago in Fuyuki City, a young boy was caught in a massive inferno that incinerated his parents and consumed a large portion of the city; as he was dying, a man saves him. Now this boy, Shirou Emiya, is an amateur mechanic who attends school at Homurabara Gakuen. Shirou also seems to be quite a bit of a magician but his abilities are no where near the level of his late father's. Meanwhile, the city is beginning to be plagued by gas spills and homicides and with Shirou's sense of justice starts to kick in, what could someone like him possibly do?

Rin seems to have problem with the servant she has and the fact that she wasn't powerful enough to call forth a more powerful servant. Back at school, Shirou has been asked by Ayako to keep an eye on Sakura's brother Shinji Matou, who's been fooling about in archery club. In the end Shinji takes advantage of Shirou's helpful nature and makes him take care of the archery club's dojo. However while Shirou's cleaning head goes out to inspect a noise, only to witness a fight between two servants.

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.

Saber and Shirou practice for a bit, Saber completely dominating over Shirou and not training how some would think but just a straight out attack between the two of them where Shirou keeps getting hit and slammed to the floor multiple times. Saber comments on how Shirou is doing fairly good and she is amazed by his zeal and things. Thy take a break and Shirou asks Saber what wish she wants granted if she got the Holy Grail.Shirou heads out to buy things for lunch and he runs into Ilya. They talk for a bit about their past and Ilya says where she came from. Shirou tells her that he inherited something precious from him. He says how he didn't receive his fathers Magic Mark but says he is still a master, just a half-assed magician.Shirou gets home, he talks with Rin who says at school Shinji asked her to team up with him. Rin says she rejected him though, saying she was already partnered with Shirou and she trusts him a lot more.Archer says how much of a failure Shirou is and that he would never be able to defeat a Servant. He does however seem to give him some advice saying that, If you cannot defeat someone, imagine something in your head you can defeat them with, for that is all you will be able to do.

Shirou falls asleep and sees a dream of a flashback of Saber's past. We see Saber in plain olden time cloths walking up to a sword in a stone.Saber wakes up and notices Shirou is gone. She talks to Rin and despite Archer's objection they go looking for him, suspecting he has been kidnapped by an enemy.Shirou wakes up in Ilya's house as her captive. Ilya says how she wants Shirou to become hers.

Shirou wakes up after having yet another dream of Saber's past and is clearly shaken up by what happened. That morning, during breakfast, Ilya is introduced by Rin as another person to be staying there for a while and Taiga seems to accept it well. Meanwhile there have been news on even more gas leaks, meaning that the Master at Ryudouji seems to be escalating his plans. While Shirou, Rin and Saber are planning what to do about this, Ilya enters the room with a great deal of information on this topic.

Saber can't seem to get Shirou of her mind but that is short lived when she finds out from Rin that Ilya has a terrible fever and may not last long. Meanwhile Shirou is still missing, having not returned from the night before and Saber knows that there's only one place he could be, the church. It doesn't take long for Saber to notice the wounded Shirou on the floor but she's unable to do anything because she's greeted by Lancer. Saber must decide whether she truly desires the Holy Grail as she's given a means in acquiring it.Kirei Kotomine reveals what really happened at the end of the last Holy Grail War and what will Shirou and Saber do knowing the true meaning of the Holy Grail?