On the 10th anniversary of the great fire of Fuyuki City, Rin Tohsaka performs the summoning ritual and summons Archer. Archer soon fights Lancer, but their fight is witnessed by Shirou Emiya who flees but is found by Lancer and killed. Rin uses her necklace to revive Shirou but he is later attacked again by Lancer and inadvertently summons Saber, who drives Lancer off. At a church, Kirei Kotomine tells Shirou about the Holy Grail War and he decides to fight. Shirou proposes an alliance to Rin, but they are interrupted by Illyasviel von Einzbern and Berserker. A fight ensues which Archer ends with a massive explosion. Illya withdraws and Shirou collapses from his injuries.
The next day, Shirou gets a weird feeling upon entering the school and meets with Rin to investigate. They encounter Rider and her master, revealed to be Shinji Matou. Rin saves Shirou while Shinji flees into the school. Shirou summons Saber and they find Shinji huddled in the corner of a classroom with a defeated Rider who disappears. Shinji claims that someone else did it and flees again. Later, Kotomine offers Shinji a new servant.
That night, Shirou sleepwalks to Ryuudou Temple where Caster attempts to take his command spells. Saber follows but is stopped by Assassin while Shirou is saved by Archer who then engages and overpowers Caster, sparing her life. Shirou argues with Archer, who tells Shirou to accept that he cannot save everyone. Ignoring him, Archer turns on Shirou before being rescued by Saber. Returning home, Rin, Shirou, and Saber are ambushed by Caster who stabs Saber with Rule Breaker, a weapon that nullifies servant contracts. Saber resists Caster’s commands to kill Rin and Shirou before disappearing with Caster. Caster kills Kotomine and takes over the church and Rin and Archer soon confront Caster and her master Souichirou Kuzuki, but Archer betrays Rin. Shirou intervenes before Archer tells Caster to spare them. Outmatched, the two decide to request Illya’s assistance.
Shirou and Rin arrive at Illya’s castle to find Illya and Berserker being attacked by Shinji and his new servant Gilgamesh, who defeats Berserker and rips Illya’s heart out. Rin and Shirou confront Shinji who offers them a chance to join him which they refuse, and Shinji and Gilgamesh retreat. Following a short argument, Rin and Shirou encounter Lancer, from whom they accept an offer of assistance.
Returning to the church, Lancer engages Archer while Rin and Shirou engage Caster and Kuzuki. The two are suddenly saved by Archer who kills both Caster and Kuzuki, then resumes his attack on Shirou. Rin forms a new contract with Saber and Archer reveals a reality marble called Unlimited Blade Works. Archer unleashes a hail of swords at Shirou and Saber and takes the opportunity to kidnap Rin. Shirou demands Archer to confront him at the Einzbern Castle.
Later, Shirou confronts Archer and deduces from Rin’s earlier comment that Archer is actually Shirou’s suicidal future self, who seeks to kill Shirou to end his own regretful existence. Shirou and Archer begin their fight while Lancer rescues Rin from Shinji and Kotomine, who reveals that he is alive and is Lancer’s master. When Lancer refuses to kill Rin, Kotomine forces Lancer to commit suicide. Before dying, Lancer impales Kotomine from behind, scares Shinji away, unties Rin, and sets fire to the castle. Shirou experiences a vision of the future that awaits him but continues the fight regardless, defeating Archer and declaring that he will not regret what awaits him. Gilgamesh suddenly interrupts the fight and critically wounds Archer before withdrawing due to the fire. Rin later transfers a part of her magical seals over to Shirou so that he can utilize Unlimited Blade Works to counter Gilgamesh. Elsewhere, Gilgamesh implants Illya’s heart into Shinji and he mutates into a large mass.
Arriving at Ryuudou Temple, Saber fights Assassin while Shirou and Rin confront Gilgamesh. Saber helps Rin defeat Assassin and Shirou activates Unlimited Blade Works. Rin rescues Shinji and is about to be trapped until Archer intervenes. Saber uses Excalibur to destroy the unfinished Holy Grail and disappears, having exhausted her magical energy. Meanwhile, Shirou overpowers and severs Gilgamesh’s arm. This causes a void to open from the wound that begins to consume Gilgamesh. He attempts to take Shirou with him, but is defeated by Archer. Rin reunites with Archer, who tells her to look after his younger self. She promises to do so, and Archer disappears. With the war concluded, life resumes as normal, and Rin and Shirou begin a romantic relationship.