In the series' backstory, 102,000 years ago in a place that would be modern-day Mexico, it started with a mysterious but powerful race with incredibly long lifespans and the ability to absorb life forces from plants and animals, although they had the disadvantage of being easily disintegrated if exposed to sunlight and thus lived underground instead. Kars, an underground-dwelling humanoid being known as a Pillar Man, created a stone mask which grants immortality by absorbing life energy to conquer the sun (which kills his kind). However, the stone mask cannot penetrate his head and unlock Kars' true potential. As he tirelessly slaughtered things for blood to activate the stone mask, his tribe begins to fear Kars for his obsession. When his tribe says Kars must be killed, Kars is angered and questions them if they want to conquer the sun. If they objected, Kars would say they will die. As his tribe attempts to kill him, Kars and his companion Esidisi fight back. He slaughtered all but four of the tribe.

In Fuyuki City, a long-lived ritual involving battles between seven magi and their servants is taking place. This ritual is known as the Holy Grail War and it promises to grant the victor any wish. With the war now entering its fifth iteration, the stage is set for Rin Toosaka to succeed her father's legacy. Rin wishes to summon Saber, said to be the most powerful class. But when she miscalculates and summons Archer instead, how will she fare in the battles that lie ahead of her? [Written by MAL Rewrite]

As the Fifth Holy Grail War reaches its conclusion, Saber repeats her final duty from the previous war in order to end the vicious cycle once and for all. With the decisive blow draining her remaining mana reserves, Saber's body begins to dissipate. She utters a tearful farewell—but Rin Toosaka reaches out to her at the last moment. The future has been changed, and a new beginning awaits. [Written by MAL Rewrite]

Fleeing from the consequences of his decision at the Hell's Gate, superpowered Contractor Hei and his companion Yin take refuge in a quiet inn, adopting the guise of a married couple in order to not draw suspicion. In an attempt to recover from recent events, Hei befriends the inn's other guests. He discovers that one of them is a fellow Contractor tasked with killing him. Their resulting encounter spells disaster for both Hei and Yin, who are forced to fight for their lives and grapple with the emotional wounds sustained in their previous life together. [Written by MAL Rewrite]