The story takes place in an ordinary Japanese town, Fuyuki City. Hidden from society, there has been a deadly war going on in this town. Seven sorcerers known as "Masters" summon powerful familiars called "Servants," and they all fight each other till the last one. The last one is said to attain the Holy Grail, which will grant them a wish. Only a few know when this War started and what the Holy Grail is, but the war is about to begin again this year.
The main character is Emiya Shirou, who lost his parents in a fire and was adopted by a man who called himself a sorcerer. Admiring his stepfather, he has been training himself to be a sorcerer. However, he had no talent and he could barely use even one type of sorcery. His stepfather has already passed away, and today he's a sorcerer without any skills or knowledge. He is involved in the War of the Holy Grail when he accidentally summons Saber, who is said to be the strongest servant of all. That a war is waging among some chosen magi, and that he is about to become its focal point.

Based on the third route of the 2004 visual novel.