Shirou Emiya lost his parents in a fire when he was young and was later adopted by a sorceror by the name of Kiritsugu Emiya. Although he was full of admiration for his adopted father and yearns to become an ally of justice, Shirou has limited powers and was unable to become a strong sorceror like his father. That is until one fateful day, he was drawn into the Holy Grail War and had to summon a female "Servant" known as Saber in order to protect himself. It turns out that the Holy Grail War involves a series of battles among powerful sorcerors to fight for the possession of a relic that will grant one's wishes, the Holy Grail. There are altogether seven "Masters" who can summon their respective "Servants" from different classes known as Saber, Archer, Rider, Berserker, Lancer, Caster and Assasin. These "Servants" have to hide their names in order not to reveal their weaknesses to the enemies. The story revolves around Shirou and his entanglement in the Holy Grail War.
"The fourth true ancestor" is a legendarily strong vampire that shouldn't exist. Accompanied by the 12 "gun-beasts," this phantom vampire is said to have appeared in Japan. In order to find and kill this "fourth true ancestor," the government and the Lion King Organization order the dispatch of attack mages called "sword-maidens." For some reason an apprentice named Yukina Himeragi was chosen for the task. Wielding the strongest spiritual spear, Yukina comes to the special demon district Itokami City. There she encounters Kojou Akatsuki and learns the true nature of the "fourth true ancestor."
In the "Great Disaster," Japan has been thrown into chaos by onmyouji (a kind of magician). Harutora Tsuchimikado was born into an onmyouji family, but has no power whatsoever. His childhood friend Natsume (another member of the Tsuchimikado family) appears to him one day to take him up the promise he made long ago to become her shikigami (familiar). A battle between onmyouji is about to begin.