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