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The story of Fate/stay night revolves around the main protagonist Shirô Emiya, a young male high school student. When Shirô was a child, his father told him how he had failed at his life ambition to become a "Hero of Justice". Shirô affirms to his foster father that he intends to devote his life to achieving that distant ideal, much to Kiritsugu's chagrin. To do this, Shirô pleads with a begrudging Kiritsugu to teach him sorcery; but being born without the capabilities of a magus, Shirô proves to be talentless in almost all the fundamental sorcerous disciplines.

When the story begins, Fuyuki City is the setting for a secret and violent war among competing magi. For the past two centuries, seven sorcerers have gathered and engage in a Battle Royale, each gambling his or her own life to obtain the Holy Grail, a legendary chalice capable of granting wishes. The past four Holy Grail Wars have typically occurred every sixty years, with the most recent concluding a decade ago, but the fifth war has started prematurely.

Each of the sorcerers, better known as Masters, is aided by one of the seven summoned spiritual familiars known as Servants, who are the reincarnations of legendary souls from all across time. These resurrected souls, possess superhuman characteristics and wield powerful artifacts or abilities called Noble Phantasms. Only one Servant can be summoned in each war from one of seven classes: Saber, Archer, Lancer, Berserker, Rider, Assassin, and Caster.

After cleaning his school's kyûdô dojo late one night, Shirô stumbles upon two Servants, Archer and Lancer, battling in the school courtyard. To avoid compromising the war's secrecy, Lancer hunts down and pierces Shirô's heart with his Noble Phantasm Spear. Shirô is then discovered near death by Rin Tôsaka and because of his relationship with her sister Sakura Matô, she uses an heirloom filled with concentrated magic, Mana, to restore his damaged heart and leaves before he awakens. Shaken and dazed, Shirô picks up the heirloom and returns home only to be assaulted a second time by Lancer. Shirô weakly defends himself against Lancer using posters he turns to metal with magic reinforcment, but is soon overwhelmed by the powerful Servant's attack, and is sent flying into his shed. Cornered, Shirô prepares for the worst; but before Lancer can inflict another fatal blow, a magical mark on Shirô's hand begins to light up and a summoning circle used previously by his foster father inside the shed begins to glow. A young woman clad in armor with an invisible sword is summoned and blocks Lancer's attack. After driving Lancer away from Shirô, she introduces herself as "Servant Saber".