The Holy Grail War: a violent battle between mages in which seven masters and their summoned servants fight for the Holy Grail, a magical artifact that can grant the victor any wish. Nearly 10 years ago, the final battle of the Fourth Holy Grail War wreaked havoc on Fuyuki City and took over 500 lives, leaving the city devastated. Shirou Emiya, a survivor of this tragedy, aspires to become a hero of justice like his rescuer and adoptive father, Kiritsugu Emiya. Despite only being a student, Shirou is thrown into the Fifth Holy Grail War when he accidentally sees a battle between servants at school and summons his own servant, Saber. When a mysterious shadow begins a murderous spree in Fuyuki City, Shirou aligns himself with Rin Toosaka, a fellow participant in the Holy Grail War, in order to stop the deaths of countless people. However, Shirou's feelings for his close friend Sakura Matou lead him deeper into the dark secrets surrounding the war and the feuding families involved.

In Fuyuki City, the Fifth Holy Grail War is about to commence a lengthy battle of blood, death, and misery. High school student Rin Toosaka has trained her entire life for this moment—to become a magus capable of being a Master in the war. Summoning her Servant known as Archer, Rin finally sets foot into the battle. Discovering that one of her acquaintances, Shirou Emiya, is drawn into the war as well, Rin offers to form an alliance for the time being. And as the two of them grow closer, Rin begins to learn more about Shirou's fate and ideals. Nevertheless, her goal remains the same: to win the all-powerful relic that can fulfill the wishes of those who are victorious after the war—the Holy Grail.

After succumbing to an unenviable fate, Kiritsugu Emiya has left Shirou Emiya the duty to save mankind in his place. The world is dying and time is ticking, but when the salvation Shirou seeks is at the cost of his only family left—his younger sister—will he still have the heart to pursue this duty? Shirou is now pressed with the choice to continue being a hero of justice—or become the very evil his ideal has vowed to vanquish. The orphan is alone once again, yet his body is still made of swords. The Fifth Holy Grail War now begins with his oath under snow.

After a mysterious inferno kills his family, Shirou is saved and adopted by Kiritsugu Emiya, who teaches him the ways of magic and justice. One night, years after Kiritsugu's death, Shirou is cleaning at school, when he finds himself caught in the middle of a deadly encounter between two superhumans known as Servants. During his attempt to escape, the boy is caught by one of the Servants and receives a life-threatening injury. Miraculously, he survives, but the same Servant returns to finish what he started. In desperation, Shirou summons a Servant of his own, a knight named Saber. The two must now participate in the Fifth Holy Grail War, a battle royale of seven Servants and the mages who summoned them, with the grand prize being none other than the omnipotent Holy Grail itself. Fate/stay night follows Shirou as he struggles to find the fine line between a hero and a killer, his ideals clashing with the harsh reality around him. Will the boy become a hero like his foster father, or die trying?