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?

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.

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 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?

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.

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.

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 takes Saber out on a date to try and convince her not to use the Grail and go back to her own time, but to stay in this time instead.