The series features several major twists culminating in its bittersweet conclusion:
- The Nature of the Holy Grail: The Holy Grail is not a benevolent artifact; it was tainted in the previous war by the spirit All the World's Evil (Angra Mainyu), meaning any wish granted will inevitably manifest through apocalyptic destruction and slaughter.
- Kirei Kotomine and Gilgamesh's Survival: Kirei Kotomine was never a neutral supervisor; he secretly survived the Fourth Holy Grail War alongside Gilgamesh, feeding Gilgamesh the life force of orphaned children beneath the Fuyuki Church while orchestrating the Fifth War to bring about the Grail's catastrophe.
- The Truth of Avalon: The reason Shirou survived the fire and can rapidly regenerate from mortal wounds is that Kiritsugu implanted Saber’s sacred scabbard, Avalon, into Shirou’s body a decade ago.
- The Final Climax: Shirou returns Avalon to Saber, giving up his passive immortality to restore her supreme absolute defense. Saber invokes Avalon to reflect Gilgamesh’s ultimate attack Enuma Elish and cuts him down with Excalibur, while Shirou uses his traced weapon and the Azoth blade to vanquish Kotomine. Saber then obeys Shirou's final command seal to blast and destroy the tainted Holy Grail.
- The Ending: With the Grail destroyed, Saber's contract ends. She confesses her love to Shirou before vanishing into the morning light. She awakens back in her own era on the battlefield of Camlann, orders Sir Bedivere to return Excalibur to the Lady of the Lake, and peacefully closes her eyes to rest, finally free of regret. Shirou returns to his daily life in Fuyuki, carrying the memory of Saber and continuing to walk forward into the future.