I know I say the same thing every time I watch The Zygon Inversion, but man, the ending really is incredible. Flawless writing and performances. It's politically, morally, and spiritually sophisticated. It doesn't shy from difficult truths and doesn't rest in cliches.
In a show that's usually completely uncritical of radicalism ("Are you with the rebels?" "My dear, I am ALWAYS with the rebels"), Capaldi's Doctor exhibits admirable maturity. He completely dismisses victim ideology w/the impatience of a grown-up listening to a whining teenager.
Bonnie's response to this makes sense. She assumes (reasonably misunderstanding the subtext) that he is condescending because he's ignorant and malicious. "I will not change my mind," she says to his appeal to her intelligence. She points out that her enemies won't let her go.
The Doctor, whose arguments have thus far been political and pragmatic (you can't start a war just bc life is unfair - even if you win this war, how will that achieve your goals - war is an inefficient solution to problems, etc.) senses the underlying moral need and goes for it:
In this he reveals that he's NOT just that he's trying to get the drop on her. He's NOT speaking to her from a great height. He loves her and is willing to suffer for it. (Remember: "Do you think I care for you so little that betraying me will make a difference?")
Lesser writers would have had her melt at this point. Moffat and Harness don't take the easy route. She reacts to forgiveness with pride. "You don't understand. You will never understand." Of COURSE that's how she would react.
At this point, Capaldi has a big speech about how much he understands. It's utterly convincing. You believe the man has lived through thousands of years of war. And it underlines that he isn't speaking to Bonnie from far away. He wants her to change because he understands her.
This is enough for Kate Stewart. But, again, Bonnie doesn't just automatically convert. Instead, she does something else. She's started to "think like" the Doctor JUST enough to realize that the box was always empty. She's started to understand other people. Her mind is opening.
The crisis ends. She still can't comprehend the Doctor's grace. He explains that, many years ago, he was in the same position. He had to be talked out of a terrible utilitarian genocide.

This apt reference to the Time War nicely wraps up all the loose ends in the scene.
You know, I thought this joke from earlier in the episode was just a joke. But there may be something here.
It's a near-impossible brief - how do you convincingly talk down a terrorist (she's brutally killed many before this scene) who isn't just "secretly misunderstood?" How do you do it without trickery? This scene pulls it off bc it understands human nature.
It's also a kind of crazy pivot after Capaldi has largely been playing the goofball throughout the episode. This is some serious gravitas. I don't think many (any?) other Doctors could pull it off.
Actually, I'd forgotten that impressionists and other Doctor actors have delivered this speech, so its easy to compare. Out of all of them, only the Three really works. He has the moral authority, the tendency towards speechifying, the indignation and wit.
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