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.

Saber's fight with Assassin and Shirou's fight with Souichirou reaches its climax. Souichirou shatters Shirou's blades again, sending him flying down to where Rin and Sakura are and it is upto Saber to defeat Assassin and make it down in time to save everyone. With Saber still affected by Caster's Noble Phantasm Rule Breaker, she isn't able to defeat Caster when all of a sudden their fight is interrupted by an unknown Servant. It seems that Saber is familiar with this Servant, but it turns out he's the eighth Servant in this Holy Grail War.In light of the appearance of the eighth Servant, Saber finally reveals to Shirou the shocking events of the previous Holy Grail War.

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?

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.

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?