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.

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.

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.

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.