In the city of Orario, beneath an impossibly tall tower, lies the dungeon. Only adventurers who form partnerships with the gods themselves have any hope of defeating the monsters that lie within. But the dungeon is not the only place where monsters exist. Far from Orario, in the ruins of an ancient city, a new threat arises. To counter this threat, the goddess Artemis has come to Orario in search of a champion—but it’s not Ais Wallenstein (the legendary Sword Princess) nor Ottar (the strongest warrior to ever enter the dungeon) that she chooses. Rather it is Bell Cranel, a newbie adventurer partnered with a low-tier goddess.

Shirou Emiya finds himself an unwilling participant in a deadly competition where seven Mages summon heroic spirits as servants to duel each other to the death. They compete for the chance to make a wish from the Holy Grail, which has the power to grant any wish. Shirou is unskilled as a mage and knows nothing of the Holy Grail War, but he and his servant, Saber, enter into a temporary partnership with another Mage, Rin Tohsaka. However, problems arise between Shirou and Rin's servant, Archer, who seems to seriously despise him.

Shiro Emiya is a young magus who attends Homurahara Academy in Fuyuki City. One day after cleaning the Archery Dojo in his school, he catches a glimpse of a fight between superhuman beings, and he gets involved in the Holy Grail War, a ritual where magi called Masters fight each other with their Servants to win the Holy Grail. Shiro joins the battle to stop an evildoer from winning the Grail and to save innocent people, but everything goes wrong when a mysterious "Shadow" begins to indiscriminately kill people in Fuyuki...

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 Tohsaka 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.

As Sakura drowns in the murky darkness of the sins she has committed, Shirou's vow to protect her at all costs leads him into a raging battle to put an end to the Holy Grail War. Will Shirou's wish reach Sakura even as he challenges fate itself in a desperate battle against the rising tide?