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.

After the meeting with Kirei Kotomine Shirou and Rin leave the church only to run into another Master that goes by the name of, Illyasviel von Einzbern. Saber is forced to go into combat against an incomprehensibly stronger servant, called Beserker. With Saber's previous injury still causing major problems and reducing her fighting capacity, is there even a chance of her winning?

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.

Shinji says things like how he has no intention of fighting and he was just dragged into this war. He asks to make an alliance with Shirou to go after Rin but Shirou refuses. Shinji says because he doesn't know magic other Masters can't detect him so that means Shinji isn't the other Master Rin was detecting, meaning there is a fourth one at the school. Before Shirou leaves Shinji tells Shirou about how one of the Masters has set up base at a temple.Shirou gets home and is yelled at by Saber and Rin, Rin having come over after Shirou didn't come home. Shirou tells them about Shinji and the Master at the temple.Shirou and Rin both agree, against Sabers judgment, that they should not attack the temple yet as they don't know what Servant and it may be a trap.Saber brings up again with Shirou the temple but Shirou insists that they won't be going.

Saber is eager to go to the temple but Shirō has insisted that they won't be going because it seems too dangerous. Nonetheless, as soon as Shirō falls asleep, Saber heads off by herself to the temple, not only to be confronted by the servant identified as Assassin. Unlike any other servant, Assassin actually reveals his true identity to Saber, as Sasaki Kojirou. Although the talking ends here and the fighting begins but while this is going on Rider sneaks past them and enters the temple to fight some woman. Who is this mysterious woman and was Shinji planning this all along?

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 is very worried about the well being of the students, staff, and of the school after yesterday's events, he's especially worried about Taiga who seems to be recovering well. Shirou is now determined to put an end to this and plans to go after Shinji before he can make another force field and with Sabers support they head out. However before that, Shirou has some important information to disclose to Rin about Shinji's Servant, Rider about the Noble Phantasm she used.

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.

Shirou has found himself trapped in the same place Kirei Kotomine trapped Shirou's father. Surrounded by death Shirou must escape this place through will power alone, if he want's to end this Holy Grail War once and for all. Saber is also having trouble defeating the somewhat unbeatable Gilgamesh yet there is hope, with the power of "Avalon" The Ever-Distant Utopia.What will truly come about from destroying the Holy Grail? Will things be able to go back to normal?