The Holy Grail War: a violent battle between mages in which seven masters and their summoned servants fight for the Holy Grail, a magical artifact that can grant the victor any wish. Nearly 10 years ago, the final battle of the Fourth Holy Grail War wreaked havoc on Fuyuki City and took over 500 lives, leaving the city devastated. Shirou Emiya, a survivor of this tragedy, aspires to become a hero of justice like his rescuer and adoptive father, Kiritsugu Emiya. Despite only being a student, Shirou is thrown into the Fifth Holy Grail War when he accidentally sees a battle between servants at school and summons his own servant, Saber. When a mysterious shadow begins a murderous spree in Fuyuki City, Shirou aligns himself with Rin Toosaka, a fellow participant in the Holy Grail War, in order to stop the deaths of countless people. However, Shirou's feelings for his close friend Sakura Matou lead him deeper into the dark secrets surrounding the war and the feuding families involved.

The world has become a slaughtering ground for the Crimson Denizens, mysterious beings from a parallel universe who thrive on the life energy of humans. These merciless murderers only leave behind scant remainders of souls called Torches, which are mere residues that will eventually be destroyed, along with the very fact of the victims' existence from the minds of the living. In an ambitious endeavor to put an end to this invisible, hungry massacre, warriors called Flame Hazes relentlessly fight these monsters. One fateful day, Yuuji Sakai ceases to be a regular high schooler—he becomes trapped in a crevice of time and is suddenly attacked by a Denizen. Coming to his rescue just in the nick of time is a nameless hunter who seems no different from an ordinary young girl except for her blazing eyes and burning crimson hair. However, before Yuuji can learn anything more about his situation, he discovers that he has already been reduced to a Torch—merely a scrap of memory waiting to be extinguished.

The Holy Grail is a powerful, ancient relic capable of granting any wish the beholder desires. In order to obtain this power, various magi known as masters summon legendary Heroic Spirits called servants to fight for them in a destructive battle royale—the Holy Grail War. Only the last master-servant pair standing may claim the Grail for themselves. Yet, the third war ended inconclusively, as the Grail mysteriously disappeared following the conflict. Many years later, the magi clan Yggdmillennia announces its possession of the Holy Grail, and intends to leave the Mage's Association. In response, the Association sends 50 elite magi to retrieve the Grail; however, all but one are killed by an unknown servant. The lone survivor is used as a messenger to convey Yggdmillennia's declaration of war on the Association. As there are only two parties involved in the conflict, the Holy Grail War takes on an unusual form. Yggdmillennia and the Mage's Association will each deploy seven master-servant pairs, and the side that loses all its combatants first will forfeit the artifact. As the 14 masters summon their servants and assemble on the battlefield, the magical world shivers in anticipation with the rise of the Great Holy Grail War.

Sung Jin-Woo, dubbed the weakest hunter of all mankind, grows stronger by the day with the supernatural powers he has gained. However, keeping his skills hidden becomes more difficult as dungeon-related incidents pile up around him. When Jin-Woo and a few other low-ranked hunters are the only survivors of a dungeon that turns out to be a bigger challenge than initially expected, he draws attention once again, and hunter guilds take an increased interest in him. Meanwhile, a strange hunter who has been lost for ten years returns with a dire warning about an upcoming catastrophic event. As the calamity looms closer, Jin-Woo must continue leveling up to make sure nothing stops him from reaching his ultimate goal—saving the life of his mother.