Academy City. An independently governed City 30 years ahead of the future in science and technology, land locked in Japan, made up mainly of high schools, colleges, labs, and possessing a population mainly comprising of students and teachers. 60 percent of these students possess psychic powers and live as espers.. and one of the 7 most powerful of these espers, The Railgun, Mikoto Misaka, lives in this city. Mikoto has been orphaned for about 1 month now. Following the death of her family by unknown causes, she has been debating leaving Academy City to study in America. However, things change when she finds herself baring witness to two strange warriors called Archer and Assassin battling it out. And to make matters stranger, she is saved by a mysterious knight calling herself Saber. The Grail Wars of Academy City are about to begin.

The Holy Grail War is no more, and all the Servants are living in peace with their Masters. However, when Rin Tohsaka gets a call from her Guardian, proclaiming two Servants suddenly appeared, saying they want to see Saber. When Saber realizes who they are, a new Servant suddenly appears proclaiming she is stronger than Saber, and the rest of the Servants. With her comrades, the new Servant challenges everyone to a Holy Grail War. Will the Servants and their Masters accept her offer and if so...Are they prepared for what the new Servant has in store?