On the 10th anniversary of the devastating fire that ravaged Fuyuki City, Rin Tohsaka begins her summoning ritual and successfully calls forth Archer. Immediately, Archer is embroiled in a conflict with Lancer, a battle that catches the attention of Shirou Emiya, who, in a panic, tries to escape. Unfortunately, Lancer finds him and ends his life. However, Rin, determined to save Shirou, uses a special necklace to revive him. Soon after, Shirou is attacked once again by Lancer, inadvertently summoning Saber, who swiftly drives Lancer away.
At a nearby church, Kirei Kotomine takes the opportunity to explain the nature of the Holy Grail War to Shirou, who decides to join the fray. He proposes an alliance with Rin, but their plans are interrupted by Illyasviel von Einzbern and her formidable servant, Berserker. A fierce confrontation ensues, and Archer brings it to a head with a tremendous explosion, causing Illya to retreat while Shirou succumbs to his injuries.
The following day, Shirou feels a sense of foreboding upon entering school and decides to investigate alongside Rin. They encounter Rider and her master Shinji Matou, who initially appears threatening but is ultimately saved by Rin when Shinji flees into the school. Shortly thereafter, Shirou summons Saber, and the two confront Shinji, who is hiding in a classroom with a defeated Rider, only for Shinji to scurry away again, claiming innocence. Meanwhile, Kirei Kotomine extends an offer to Shinji to acquire a new servant.
That night, while sleepwalking, Shirou finds himself at Ryuudou Temple, where Caster tries to seize his command spells. Saber rushes to follow him but is intercepted by Assassin, leaving Shirou under Archer's protection. As the confrontation unfolds, Archer manages to overpower Caster but spares her life, leading to a clash of ideologies between him and Shirou. Archer, frustrated with Shirou's idealism, warns him that he can’t save everyone, only for Shirou to remain steadfast in his beliefs. This conflict comes to a head when Archer turns on Shirou, but Saber intervenes just in time.
Back at home, the trio finds themselves ambushed by Caster, who uses her weapon, Rule Breaker, to stab Saber, nullifying their contract. Despite Saber's struggle, she resists Caster's command to eliminate Rin and Shirou before vanishing along with Caster. In the aftermath, Caster kills Kirei and takes control of the church, forcing Rin and Archer to confront her and her master, Souichirou Kuzuki. Just when the situation appears dire, Archer betrays Rin, but Shirou intervenes, leading to a precarious alliance with Illya.
As Shirou and Rin arrive at Illya's castle, they find her besieged by Shinji and his new servant, Gilgamesh. In the ensuing struggle, Gilgamesh overpoweringly defeats Berserker and rips Illya's heart from her chest. In the wake of this chaos, Rin and Shirou refuse Shinji's offer of alliance, leading to their swift retreat. Shortly after, they decide to join forces with Lancer, hoping to overcome the growing threats.
Returning to the church, Lancer faces Archer while Rin and Shirou confront Caster and Kuzuki. In a dramatic twist, Archer eliminates both Caster and Kuzuki, only to refocus his wrath on Shirou. Under escalating tensions, Rin establishes a new contract with Saber, while Archer launches an onslaught of swords through his reality marble known as Unlimited Blade Works. During the chaos, he abducts Rin, prompting Shirou to challenge him at the Einzbern Castle.
In the climactic encounter, Shirou deduces that Archer is, in fact, a future version of himself, plagued by regret. As their conflict intensifies, Lancer intervenes to save Rin from Shinji and Kirei, who shockingly reveals his survival and manipulation over Lancer. In a heartbreaking moment, when Lancer refuses to kill Rin, he is forced into suicide by Kirei, but not before he manages to punish Kirei and free Rin. Amidst the ruins, Shirou envisions a harrowing future but remains resolute in his fight against Archer, determined not to succumb to despair.
The arrival of Gilgamesh abruptly disrupts their battle, severely injuring Archer before retreating in the chaos of fire. Later, Rin helps Shirou harness the magic of Unlimited Blade Works, arming him for the fierce showdown against Gilgamesh. Following a series of fierce battles, Saber faces Assassin with assistance from Shirou and Rin. In a final act of self-sacrifice, Saber destroys the unfinished Holy Grail, using up her remaining energy, while Shirou succeeds in severing Gilgamesh's arm, triggering a cataclysmic void.
In the denouement, with the stakes high, Archer assists Shirou in defeating Gilgamesh but disappears shortly after, having fulfilled his purpose. With the conflict resolved, Shirou and Rin find solace in each other, embarking on a new chapter together as their lives gradually return to normalcy.
