Kisah ini pada saat Perang Cawan Suci dan menguak hubungan antara Shirou Emiya dan Sakura Matou, dua remaja yang terlibat dalam konflik ini. Kisah berlanjut dari Takdir Fate/stay night: Heaven's Feel I. presage flower, mengikuti Shirou saat ia terus terlibat dalam Perang Cawan Suci bahkan setelah dieliminasi sebagai master.

The story focuses on the Holy Grail War and explores the relationship between Shirou Emiya and Sakura Matou, two teenagers participating in this conflict. The story continues immediately from Fate/stay night: Heaven's Feel I. presage flower, following Shirou as he continues to participate in the Holy Grail War even after being eliminated as a master.