Illyasviel von Einzbern is a normal schoolgirl in Japan. She lives with her overachieving nice guy older brother Shirou Emiya and her two maids, her parents are perpetually out of the country, and she has fanciful dreams of using magic to make her dreams of love with Shirou come true. Enter fierce rivals Rin Tohsaka and Luviagelita Edelfelt, two Magi who have been sent to Japan by Zelretch the Wizard Marshall, Master of Parallel Worlds, with the powerful sentient Kaleidosticks to collect the mysterious Class Cards and clean up their mess. After getting fed up with their constant infighting, one Kaleidostick, Magical Ruby, senses Illya's fleeting dream of magic and leaves Rin for her, tricking her into becoming a magical girl. Now Illya is being forced by Rin to collect the dangerous Class Cards in her place. But perhaps more dangerous still are Illya's own mysteries that may have unknowingly attracted Ruby to her.
It has been a month since Illya and Miyu became magical girls and sealed all of the Class Cards. Rin and Luvia have been forced to remain in Japan to clean up the aftermath, such as the now-unstable magic in the area's ley lines. While helping with the cleanup, the seal on Illya's mysterious innate magic goes berserk and she loses control of her transformation. By the time she has realized what happened, a mysterious girl who looks eerily like Illya appears, apparently bent on bringing destruction down on the original whose heart she seems to have spawned from, and making matters worse she holds the power of the Archer Class Card, with which Illya holds a special bond, within her body.
Shirou Emiya lost his parents in a fire when he was young and was later adopted by a sorceror by the name of Kiritsugu Emiya. Although he was full of admiration for his adopted father and yearns to become an ally of justice, Shirou has limited powers and was unable to become a strong sorceror like his father. That is until one fateful day, he was drawn into the Holy Grail War and had to summon a female "Servant" known as Saber in order to protect himself. It turns out that the Holy Grail War involves a series of battles among powerful sorcerors to fight for the possession of a relic that will grant one's wishes, the Holy Grail. There are altogether seven "Masters" who can summon their respective "Servants" from different classes known as Saber, Archer, Rider, Berserker, Lancer, Caster and Assasin. These "Servants" have to hide their names in order not to reveal their weaknesses to the enemies. The story revolves around Shirou and his entanglement in the Holy Grail War.
Ten years ago, the magus Kiritsugu Emiya saved one lone survivor of a great disaster. As he cried in happiness, he proclaimed that by saving him, he had saved himself. The boy swore then that he would become a hero who lived to save others. Five years after the death of his foster father, Shirō Emiya finds himself drawn into a battle to the death between seven magi called Masters, where each commands the spirit of a hero of legend called a Servant in pursuit of having one wish granted by the legendary Holy Grail. In this battle, Shirō will finally have the chance to face the ghosts of his past, and to find his path to face his dreams and his future. Through the power of the Holy Grail, his wish will finally come true, for a hero of justice must have an evil to defeat.