In the regional Japanese city of Fuyuki, an ancient ritual known as the Holy Grail War takes place every few decades. The Holy Grail, a legendary artifact said to grant any wish, appears to summon seven magi, who each contract with a heroic spirit reborn as a Servant. These Servants belong to seven classes: Saber, Lancer, Archer, Rider, Caster, Assassin, and Berserker. The pairs fight to the death until only one remains.

Rin Tohsaka, a young and gifted magus from a prestigious family, is prepared to follow her late father Tokiomi’s legacy and win the Fifth Holy Grail War. She attempts to summon the strongest Servant, Saber, but instead summons an arrogant and mysterious Archer who has forgotten his own name. On the first night of the war, Rin and Archer witness another Servant, Lancer, attacking a boy at their school. To hide the existence of the war, Lancer fatally wounds the boy, Shirou Emiya. Rin saves his life using her pendant, a decision that binds her fate to his.

Shirou, an orphan who survived a devastating fire years ago, was adopted by the late magus Kiritsugu Emiya. He has dreamed of becoming a “hero of justice” ever since, though his magical training is incomplete. After being dragged into the war, Shirou accidentally summons his own Servant, Saber, a powerful knight wielding an invisible sword. At the local church, the priest Kirei Kotomine explains the rules of the war, and Shirou reluctantly agrees to participate as the seventh Master, hoping to prevent another tragedy like the fire that destroyed his childhood.

Despite being enemies, Rin and Shirou form a temporary truce to survive the night. They are immediately attacked by Illyasviel von Einzbern and her monstrous Servant, Berserker. Saber holds her own, but Archer suddenly fires a massive sword-like arrow, nearly hitting both Saber and Berserker. Shirou saves Saber and passes out from exhaustion. When he wakes, he begins training with Saber while trying to keep his friend Sakura Matou and his guardian Taiga Fujimura unaware of the deadly conflict in their city.

The truce between Rin and Shirou deepens when they discover a bounded field erected over their school designed to drain life energy from innocent students. The mastermind is Shinji Matou, Sakura’s arrogant brother, who commands the Servant Rider. Shirou refuses Shinji’s offer of an alliance. While investigating the source of the field, Shirou and Rin find Rider already killed by an unknown enemy. Shinji flees, revealing a deeper conspiracy involving the cunning Servant Caster and her mysterious Master.

At the mountain temple, Caster attempts to steal Shirou’s Command Spells. Archer arrives to save him, but the rescue comes with a violent cost. Archer despises Shirou’s naive ideals. When Shirou rejects Archer’s cynical willingness to sacrifice innocent lives to achieve victory, Archer betrays his Master’s truce and tries to murder Shirou, forcing Saber to defend her Master against him. Rin uses a Command Spell to force Archer to obey, but the bond between Rin and her Servant is shattered, leaving Shirou to question whether his dream of saving everyone is a noble goal or a curse that will destroy him. The manga also includes non-canon bonus chapters at the end of each volume, collected as Tohsakabe, which depict humorous alternate scenarios where Rin summons different Servants.