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.

Shirou is still lost and incredibly confused, after seeing an elegant warrior with the name Saber appear before him and choosing him as her Master. Shirou isn't even given a chance to get to grips of the situation before Saber continues her fight with Lancer, but before things get too serious Lancer walks off. Saber then chooses to pick a fight with Rin and her servant, but Saber reluctantly accepts Shirou's order to stop. Shirou then learns of the Holy Grail War, which he has gotten himself into.

Shirou introduces Saber to Sakura and the one teacher saying she is a distant relative. The teacher tests Saber's skills to be able to defend Shirou rather pathetically, she allows her to stay at the house with him.Rin and Archer are talking he asks her why she doesn't go after Shirou, an easy target to kill. She says if he were to show up in front of her without being aware of it, she would kill him.At school some girls are missing from school for the second day in a row. After school, Shirou has stayed to investigate these disappearance when he runs into Rin. Rin confronts Shirou calling him an idiot for idly walking around without his Servant and she attacks him. Shirou runs from her and locks himself in a classroom. Shirou does the only magic he knows and fortifies a desk to protect against an attack from Rin. The whole school is being lit by this happenings, all this being watched by a mysterious character in the trees and the episode ends.

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 yelled at Shirou for not summoning her when he was in danger. Saber starts to go to school with Shirou. When Rin appears and says she will walk with Shirou to school, Saber allowing this after Rin talked to her. She explained that this way enemies may think it's a trap to not see Saber with him so they are less likely to attack.Rin explains that there should be spell marks around the school and if they destroy those it will delay the activation of the force field but not destroy it, and most likely force the master out of hiding. After school Shirou and Rin work to find spell marks and destroy them. They end up destroying a good amount of them and call it a night.On the way home, before Shirou gets anywhere but after Rin leaves he feels something really strong. He goes to investigate it and feels its coming from the archery club.

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.

After a mornings training session with Saber, Shirou is then straightaway dragged off by Rin for some more training of her own. While this is going on Shirou receives a phone call from Shinji, asking Shirou to meet him at the school. Because it seemed urgent Shirou heads of to school and is greatly shocked by what he sees. Shinji shows his true colors and says how he wanted to show Rin how he was superior to Shirou and that he would defeat him here. What will happen to Shirou and does he have the will to fight off a Master and his Servant, alone?

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.

Rin, Saber and Archer just outside of Ilya's mansion. They see Ilya walk out so they soon head inside to rescue Shirou.Rin asks Archer to slow Berserker down by himself while the rest of them escape. Archer says fine but asks if it's ok to kick Berserker's ass while doing so. Rin kind of smiles and they run off, leaving Archer to fight Berserker. Before they leave Archer yells out Emiya Shirou. Shirou stops and Archer tells him, Get this straight: You are not one who fights. You're nothing more than one who creates. Throw irrelevant thoughts away. There's only one thing you can do. Master that one thing! Archer then causes part of the ceiling to fall separating them so that Shirou will run away.The fight between Archer and Berserker commences.

Archer has been defeated by the unbeatable Beserker and now Shirou, Saber and Rin are trying their best to escape the same fate. They are able to find shelter to bide some time, because Shirou has to find a way to replenish Saber's mana while Ilya looks for them. With Archer's sacrifice, Rin is that much more determined to get out of this alive and comes up with an elaborate plan. The beginning of a fight between Saber and Berserker commences.

The battle is at the turning point, where Rin is about to be squashed by Beserker and Saber is unable to save her. As a last resort Saber decides to use her Noble Phantasm to defeat Beserker, no matter how it would affect her. Realizing that Saber could disappear from this, Shirou forces her to stop and decides to take matters into his own hands.The advancement of Shirou's character as we find what he is really able to do.

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.

With the appearance of the mysterious Archer-class Servant, Saber tells Shirou to escape while keeps him occupied. However Shirou, knowning that Saber couldn't defeat him before, foolishly tries to attack him head on and with the snap of his fingers Shirou is quickly defeated. Will Saber have the strength to defeat him, esepecially now knowing his true identity; owner of all the world's treasures, the King of Heroes of ancient Uruk, Gilgamesh.Kirei Kotomine also seems to play a major part in the Holy Grail War and it's not because he's the mediator.