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.

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?

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.

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.

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?

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?