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?

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.

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.

Shirou, Saber and Rin are at the steps to the temple.Assassin appears, he lets Shirou and Rin go past and fights Saber. Shirou and Rin head past Assassin and past him they see Sakura, in rather odd cloths who is in what seems to be pain as she is glowing red. She is in a pit arena area and as they prepare to go down there they are attacked from behind which Shirou notices and blocks the attack with Archer's swords. Souichirou appears and Shirou tells Rin to go ahead as he fights Souichirou and she goes to rescue Sakura. Meanwhile Saber and Assassin fight continues on. They compliment each other on being one of the best swordsmen they have ever faced and Assassin tells Saber that his identity, Sasaki Kojirou doesn't really exist. He is fabricated from people's minds of being a great swordsman so he is a fictional heroic soul. He says he has no desire for the Holy Grail therefore; his true desire is this, a fight with a worthy opponent.We find out more on the past of Rin & Sakura and how they once were bestfriends. Caster is watching this smiling says she just needs one magician for the sacrifice. Everything seems to be going as she had planned.

After the incident at the church, Saber and Shirou return home only to find Rin on the floor and badly injured. It turns out that Kirei Kotomine attacked her, while Shirou and Saber were occupied and that's not all because he has also taken Ilya and plans to make her the sacrifice for the Holy Grail. Aided with Rin's final advice, they both head to Ryudouji where Kirei is going to summon the Holy Grail. Saber will battle again with Gilgamesh and Shirou will have to leave her and deal with Kirei, who obviously has some sort of personal vendetta against Shirou.The final fight has just begun.