Ever since the childhood trauma that set him on his path, Emiya Kiritsugu has striven to be a level-headed, efficient, logical man. It’s partly why he kept Saber at arm’s length: an emotional connection with his Servant isn’t necessary and exposure to her illogical honor can only create inefficiencies in his plans.
So as Saber finds herself struggling with the insane anger and hatred of her former most trusted knight, essentially making her the logical one in her fight, and Iri’s body transforms into the Holy Grail, Kiritsugu never would have imagined it would not only toy with his emotions, but use his beloved logic against him.
But first, by god was I not wrong when I said the duel between Kiritsugu and Kirei would be something. It’s quite different and more minimalist than any previous battle in the show, with both participants sizing up their opponents, approaching them with a certain strategy, and switching up tactics on the fly as conditions rapidly change.
Kirei would have surely killed Kiritsugu relatively quickly were it not for Avalon imbuing Kiritsugu with a virtual “Auto-Life” status. In the slight sliver of a moment Kirei’s guard is down, Kiritsugu takes Kirei’s right arm away with Contender, and the odds are evened.
So even is the duel, in fact, that the Grail itself, runnething over with some kind of dark, blood-like ooze directly above the fighters, essentially calls a “timeout” by covering both in that ooze.
That indicates the War is finally at an end, and the Grail has chosen the victor. At the same time, Saber runs Berserker through, killing him, as Kariya also expires; claiming she cannot atone to him without winning the Holy Grail.
In an illusory world created by the Grail, an avatar of Iri representing the will of the Grail names Kiritsugu as the winner, and he need only officially pray for his wish to become reality. The only problem is, the Grail, or at least this Grail, cannot give him the miracle he wants. At least, not in a manner that is acceptable.
The Grail then sets to work taking Kiritsugu’s philosophy to its logical conclusion: killing the smaller percentage of people to save a larger one, thought-experiment style; sacrificing the few to save the many.
But if, like his time-altering battle ability, Kiritsugu would continue to whittle down some humanity in order to save another proportion, before long there will be no one left in the world but him and those he cares about the most, presented to him as Maiya, Iri and Ilya.
To save them, he’ll have to kill everyone else. In other words, “saving the world” means destroying humanity. This is the sum total of Kiritsugu’s wish, according to the Grail.
And the Grail stands ready to grant that wish, even though it is not at all what Kiritsugu wants. He rejects the Grail, unwilling to sacrifice the world for his own few loved ones, symbolically murdering both Iri and Ilya in a thoroughly upsetting scene in an attempt to subvert of the nightmare scenario the Grail put forward. The Grail curses him and he is cast out.
Back in reality, such as it is, Kiritsugu has the advantage over Kirei, who rages and fumes at him for refusing and wasting the Grail’s wish. But in killing him it seems Kiritsugu is almost doing Kirei a favor.
This Grail is not omnipotent, and thus would be no more able to reveal the nature and meaning of Kirei’s existence than it could grant Kiritsugu a miracle that would end all conflict in the world. In both cases, the one making the wish does not know what it is they seek.
That being said, the Grail is still immensely powerful and dangerous in the wrong hands, and Kiritsugu decides that no one, including him, has the right hands.
So as Saber and Archer descend on the physical Grail, poised to fight the final duel in the War, and Saber rejects Archer’s offer of marriage and servitude, Kiritsugu forsakes Saber once more, hitting her where it hurts most: he uses his two remaining Command Seals to order her to destroy the Grail with Excalibur…and she cannot disobey.
But perhaps Kiritsugu is right that Saber, like Kirei and he himself before, is merely deluding herself into believing the Grail will grant her wish, only offer shallow illusions in exchange for being possessed by someone worthy. The Grail is not an answer.