Seeking the power of the Holy Grail, something that can make miracles occur, seven different mages summon seven Heroes, and fight until the last man remains--a battle of epic proportions, the Holy Grail War. In preparation for the war, various participants are chosen from all over the globe. Eight years ago in Einzbern Castle in Germany, a girl named Illyasviel is born. Her father, Emiya Kiritsugu, embraces her knowing he will be part of the battle, as well.

Kiritsugu and his daughter Ilyasviel stroll through the Einzbern woods. As Saber watches the happy parent and child, she ponders why Kiritsugu has not spoken to her since she was summoned. And in Fuyuki City, the battle ground where the Holy Grail War will be fought, the seventh and final hero is summoned.

All the servants have been summoned and now it is a game of spy vs spy. Who will be the first to take the initiative in Fuyuki City?

Saber and Lancer fight for supremacy. After some fierce and defensive fighting from both sides, Lancer's master allows Lancer to use his noble phantasms. Lancer's magic-canceling spear and cursed spear capable to causing unrecoverable wounds catch Saber by surprise. Meanwhile, Kiritsugu is keeping watch over the fight with Maiya. Kiritsugu finds Assassin watching over the battle as well, so he decides not to act rashly. From far away, Rider and his master Waver spot the battle between Saber and Lancer. Against his master's wishes, Rider rides his Gordius Wheel down to the harbor and interrupts the battle.

Rider suddenly appears just the battle with Lancer reaches its climax, much to Saber's consternation. Undeterred, Rider calls out to the many people observing the fight from within the shadows...but it seems he's not the only heroic spirit drawn in by the battle.

A car screams down the moonlit streets of Fuyuki City, with a very happy-go-lucky Irisviel behind the wheel and a slightly unnerved Saber sitting next to her. The evening takes a bad turn when a mysterious shadow darts in front of them. The person claims to be Saber's loyal retainer, yet Saber has no memory of them...

The rules of the game have changed and the Masters have a chance to earn an extra command spell. All they have to do is find Castor and kill him.

Battle rages throughout Einzbern Castle: Kayneth's magical mercury sphere versus Kiritsugu's formidable gun arsenal, Saber and Lancer join forces against Caster in the forest, and Irisviel detects a new enemy as she and Maiya make their escape.

After having a dream of Lancer's past, El-Melloi wakes up with his body tied on a bed. Sola tells El-Melloi that his Magic Circuits were destroyed and he can no longer use magic but she also tells him to give up his Command Spells to her or she will torture him and cut off his arm. Despite Sola becoming his new Master, Lancer refuses to accept her and remains loyal to El-Melloi but Sola manages to make Lancer accept her by convincing him to fight for his old master's honor. Elsewhere, Kiritsugu decides to go hunt El-Melloi down despite Saber and Iri wishes to stop Caster. Meanwhile, Waver and Rider manages to find Caster's lair in the sewers where the former is horrified in seeing the dead bodies of Caster and Uryū victims. As Waver vomits in disgust, Rider saves his life when he kills an Assassin targeting Waver and face off two more Assassins before they escape. Now knowing Assassin is not yet dead, Waver and Rider leaves the Caster's lair but not before destroying it and burning the bodies. With Waver and Rider knowing their secret, Risei orders Kirei to send his Assassins to spy on them.

The mystery of the mass kidnappings in Fuyuki remains unsolved, with more kids disappearing daily. When Tohsaka Rin can't get in touch with her friend Kotone, she braves the darkness and enters the city on her own to search for her. That's when she spots a strange man leading two kids around and decides to follow him...

Rider, Saber, and Archer sit down for a drink and discuss what makes a King. The talk turns to violence when Assassin interrupts…

Hidden in a Fuyuki hotel, Kiritsugu tries plan his next move, but is still at a loss trying to understand Kirei's motives. Elsewhere, Iry and Saber have moved to a new hideout, a traditional Japanese manor. But while Iry seems excited about their new location, Saber senses something is amiss...

Rider and Waver make a trip into town, and stop in a bookstore along the way. There, Waver reads a biography on Rider's life and learns why he aimed to conquer the far east. Meanwhile, Caster and Ryuunosuke return to their destroyed base. A conversation with his Master leads Caster to an epiphany, and with insanity in his heart, the mad magician begins casting a certain spell...

The battle against Caster continues as the Heroes have no way of stopping him. Toki is trying to appeal to Archer to use his Noble Phantasm to obliterate the monster. Kiri meanwhile, is planning to destroy the source of the monsters powers.

As Archer and Berserker continue to battle in the sky, Saber and Rider are forced to retreat from Caster's Demon to rethink their strategy. Rider will transport the demon into Ionian Hetairoi where his armies will try to hold it off as long as they can while Saber and Lancer will have to find a way to finally destroy it. Kiritsugu calls and explains to Waver on how they will defeat the demon and tells him to inform Lancer about Saber's Noble Phantasm. Lancer realizes what Kiritsugu means and destroys his Gae Buidhe to allow Saber's wound to heal and fully use her Noble Phantasm. Tokiomi defeats Kariya by shooting a fireball, burning him and falling off from the building where he is later found by Kirei who heals him. As Berserker destroys Archer's Vimana, he now sets his sights on Saber but his jet is destroyed and driven away by Lancer and Archer respectively. With the coast clear, Kiritsugu fires a flare gun to signal to Waver where Rider should transport the demon. With the demon in position, Saber uses her Noble Phantasm, Excalibur to finally destroy Caster and the demon which the former has a vision of Jeanne before his death. With the threat over, Rider and Archer have a discussion on whether Saber's life to become King was either incredible or tragic before both of them leave with Rider hoping to duel Archer in the future and Archer now smitten with Saber.

Kayneth visits Risei and asks for his reward for Lancer helping defeat Caster. Risei agrees to reward Kayneth a Command Seal before Kayneth kills him to ensure the other Masters don't get one as well. However, Sola was kidnapped by Maiya during the battle at Mion River which she also cut off Sola's arm containing her Command Seals. As Kayneth scolds Lancer and mocks his chivalry, Saber and Iri, tipped off by Kiritsugu, arrives at Kayneth's hideout, where Saber wishes to finish her duel with Lancer which he agrees. As Saber and Lancer duel, Kiritsugu confronts Kayneth and having taken Sola hostage, gives Kayneth a magical unbinding contract that he will no longer harm or kill him and Sola if he does one thing for him; use up all of his Command Seals to force Lancer to commit suicide. Desperate to save Sola, Kayneth does so which Lancer curses everyone around him before dying. But because the contract only applies to him, Maiya snipes Kayneth and Sola, killing her instantly. As Saber ends Kayneth's suffering, she finally calls out on Kiritsugu for the terrible and dishonorable things he'll do to win which he retorts there's isn't anything honorable about chivalry and he will do everything to win to ensure his and Iri's wishes to save the world. As Kiritsugu leaves with Maiya, Iri collapses from exhaustion.

Kirei discovers Risei's body and informs Tokiomi. Kirei is saddened over his father's death, although Archer suggests that his sadness is due to not having the chance to kill his own father himself. Maiya informs Iri and Saber that Tokiomi wishes to discuss an alliance, and Iri agrees to go to the church to discuss the offer. Before his meeting, Tokiomi visits his wife and Rin, giving his daughter a spell book and some wisdom before leaving. During the meeting between Iri and Tokiomi, Tokiomi suggests a temporary alliance to defeat the other contestants first. Iri agrees, but on the condition that Kirei leaves the city and can no longer be involved in the Grail War. Tokiomi complies. As Saber, Iri and Maiya leave the church, a sickly Iri reveals to Maiya that she is actually the embodiment of the Holy Grail in human form and will die to form the Grail once the war ends. Maiya promises to protect her until that time comes. Meanwhile, Kirei is preparing to leave, but reveals to Archer that his father's dying act was to leave Kirei the remaining Command Seals, restoring Kirei's ability to be a master in the War. He also reveals the secret reason behind the war; the Holy Grail can be activated only by the sacrifice of seven Heroic Spirits. Thus, even a victorious Servant must die - which is why Tokiomi is reluctant to use his command spells, as he needs at least one to command Archer's suicide should they be triumphant. Furthermore, Kirei still wants to explore his dark desires, and Archer yearns for a more stimulating master. Later, Kirei meets with Tokiomi, who gives him guardianship of Rin should anything happen to him, and an Azoth dagger as a symbol of his completed apprenticeship. Kirei then stabs Tokiomi in the back with the dagger, telling him that, just like his own father, both men never really understood him. With Tokiomi dead, Archer and Kirei form a new contract as Master and Servant.

Years ago, a young Kiritsugu lived on an island in the Pacific with his father Noritaka and befriended a local girl named Shirley who called him Kerry. Noritaka was researching on immortality using plants with Shirley as his assistant. Despite being told by the townsfolk to stay away from Noritaka, Shirley is convinced his research will help the world and tells Kiritsugu she hopes he grows up to be great man. But one day, Kiritsugu is told by his father not to leave their home after asking him if he went into his lab. Kiritsugu ignores his father's warnings to search for Shirley only to be find her eating live chickens wildly. Shirley reveals she went into Noritaka's lab and use his immortality formula on herself which turned her into a Dead Apostle vampire who madly craves for blood. Shirley begs Kiritsugu to kill her while she can still have a hold on herself but he is unable to do it which leads her to attacking the townsfolk and turning them into Ghouls. As chaos spread throughout the island, Church Executors and Mages from the Mages Association arrive to stop and exterminate the outbreak and cover up the incident. Kiritsugu is saved from Ghouls when a gun-wielding mercenary named Natalia Kaminski saves him. Natalia explains she is there to eliminate the magus responsible for the outbreak which Kiritsugu realizes is his father. Kiritsugu confronts his father over his work and it's consequences which the latter only shrugs it off as an accident and states his plans to continue his experiments elsewhere. Angered with his father's response, Kiritsugu kills him. Emotionally broken and having nowhere to go, Kiritsugu agrees to escape together with Natalia.

Natalia has raised Kiritsugu since rescuing him from the island. He has followed her in every step in becoming an assassin. Over the years their relationship has grown to the point of mother and child, so what Kiritsugu does next is…

Irisviel time is running out and Kiritsugu is doing what he can to make her comfortable. But the game continues and he leaves to eliminate his next target. A surprise attack against his hideout leaves him a man down and heart broken.

Saber is hot on the trail of Rider, much to his delight. Meanwhile, Kiritsugu sets off on a different lead. The new player, Matou Kariya, watches in the background as his play unfolds perfectly.

The end of the battle is drawing near and relationships between Masters and Servants are changing. Many players have dropped off the field, and a very special one is next to go.

Saber vs. Berserker, Archer vs. Rider, another hero will fall and a secret will be revealed.

Two heroes, two masters, one grail; a winner will be decided.

Saber destroys the Grail along with the theater before disappearing. However, much to Kiritsugu's horror, the Grail spreads its lethal black ooze from the sky, causing death and destruction throughout half the city. With the city in flames, Kirei wakes up, surprise to be alive and to see Gilgamesh(Archer) as well. Gilgamesh reveals the ooze created a body for him and resurrected Kirei as well. Realizing the city's destruction was his wish, Kirei laughs on how abominable he is and wants to repeat it again which Gilgamesh joins him. Mortified of the destruction he seen, Kiritsugu finds joy and hope after rescuing a young boy who survived. A delusional Kariya believes he has save Sakura and reunited her with Rin and Aoi, unaware he has died falling into a pit of Crest worms under Matō estate which Sakura witness coldly. As morning arrives, Waver tells the Mackenzies he would like to stay with them while he travels around the world to find his own path. After presiding over Tokiomi's funeral, Kirei meets Rin and her mother Aoi, who survived but brain damaged, oblivious to what happen to her husband and Sakura, and gives Rin the Azoth dagger. Due to the curse and interference by the Einzberns for his failure, Kiritsugu is unable to reunite with his daughter Ilya so he decides to live in Fuyuki City and adopts the boy he rescued, Shirō. Saber finds herself where she fought her last battle during her life and cries to her knights for failing while she remembers Lancelot final words on how he regretted betraying her by having an affair with her wife Guinevere, which drove him into madness while still proclaiming his loyalty to his King. As she regrets for not understanding her people nor winning the Grail, the sun suddenly shines on her, giving her hope. Five years later, Kiritsugu tells Shirō how he dreamed to be a hero which Shirō promises his father that he will live out his dream for him. As Kiritsugu closes his eyes peacefully, he remembers the question Shirley ask