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.

The Holy Grail War is a battle royale among seven magi who serve as Masters. Masters, through the use of the command seals they are given when they enter the war, command Heroic Spirits known as Servants to fight for them in battle. In the Fifth Holy Grail War, Rin Toosaka is among the magi entering the competition. With her Servant, Archer, she hopes to obtain the ultimate prize—the Holy Grail, a magical artifact capable of granting its wielder any wish. One of Rin's classmates, Shirou Emiya, accidentally enters the competition and ends up commanding a Servant of his own known as Saber. As they find themselves facing mutual enemies, Rin and Shirou decide to form a temporary alliance as they challenge their opponents in the Holy Grail War.

In the midst of the Fifth Holy Grail War, Caster sets her plans into motion, beginning with the capture of Shirou's Servant Saber. With the witch growing ever more powerful, Rin and Archer determine she is a threat that must be dealt with at once. But as the balance of power in the war begins to shift, the Master and Servant find themselves walking separate ways. Meanwhile, despite losing his Servant and stumbling from injuries, Shirou ignores Rin's warning to abandon the battle royale, forcing his way into the fight against Caster. Determined to show his resolve in his will to fight, Shirou's potential to become a protector of the people is put to the test. Amidst the bloodshed and chaos, the motivations of each Master and Servant are slowly revealed as they sacrifice everything in order to arise as the victor and claim the Holy Grail.

As the Fifth Holy Grail War reaches its conclusion, Saber repeats her final duty from the previous war in order to end the vicious cycle once and for all. With the decisive blow draining her remaining mana reserves, Saber's body begins to dissipate. She utters a tearful farewell—but Rin Toosaka reaches out to her at the last moment. The future has been changed, and a new beginning awaits.