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.

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 Fifth Holy Grail War continues, and the ensuing chaos results in higher stakes for all participants. Shirou Emiya continues to participate in the war, aspiring to be a hero of justice who saves everyone. He sets out in search of the truth behind a mysterious dark shadow and its murder spree, determined to defeat it. Meanwhile, Shinji Matou sets his own plans into motion, threatening Shirou through his sister Sakura Matou. Shirou and Rin Toosaka battle Shinji, hoping to relieve Sakura from the abuses of her brother. But the ugly truth of the Matou siblings begins to surface, and many dark secrets are exposed. Fate/stay night Movie: Heaven's Feel - II. Lost Butterfly continues to focus on the remaining Masters and Servants as they fight each other in the hopes of obtaining the Holy Grail. However, as darkness arises within Fuyuki City, even the state of their sacred war could be in danger.

The Fifth Holy Grail War in Fuyuki City has reached a turning point in which the lives of all participants are threatened as the hidden enemy finally reveals itself. As Shirou Emiya, Rin Toosaka, and Illyasviel von Einzbern discover the true, corruptive nature of the shadow that has been rampaging throughout the city, they realize just how dire the situation is. In order to protect their beloved ones, the group must hold their own against the seemingly insurmountable enemy force—even if some of those foes were once their allies, or perhaps, something more intimate. As the final act of this chaotic war commences, the ideals Shirou believes will soon be challenged by an excruciating dilemma: is it really possible to save a world where everything seems to have gone wrong?