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.