Fuyuki City is home to an underground battle between sorcerers, each trying to obtain a powerful relic known as the Holy Grail, summoning spiritual familiars ("Servants") to do their bidding. An amateur teenage mechanic named Shirō Emiya was once thought to harbor the powers of a sorcerer, but has lived through most of his life without any connection to magic. This changed on the day when a hostile Servant attacked him, and he inadvertently summoned another one, becoming involved in the grand battle.

Fate/stay night is a visual novel. The player reads text accompanied by still anime-style images, and is from time to time prompted to make a decision that would influence subsequent events. There are three main plot arcs in the game that can be accessed through these choices, each corresponding to a female character in the game.