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 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 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.