This scene is so underrated.
The whole time after Nibiru, the atmosphere between Spock and Jim is tense. One because of Jim saving Spock, who could not understand why Jim did this. And later because he got aware of the fact, that Jim lied in his log.
Jim loses his captaincy and also his ship, what Spock doesn't even know. Until later.
Days later, after Jim telling him, that he would miss him, if he would lose Spock, our first officer can't really say anything. But he can stare at Jim like some creepy crushing schoolboy at the headquarters.
Again they don't get a moment to settle things. But Jim doesn't want to be without Spock and wants him back as his first. Something, Spock doesn't understand himself, if we read his shocked expression correctly.
On the shuttle ride, Spock is alone and deeply in thoughts when Jim comes on board. He tries to make Jim realize that the mission is anything but right. But Jim is emotional compromised. And not in the mind to make any decisions.
It's only later when Jim makes the ship wide announcement, that he realized something big.
Probably only because of what Uhura told him only moments before. Because she and Spock weren't really speaking since Nibiru. What's a big deal if they would have a functional relationship.
However. Jim is confused because he doesn't know what it is to do something without Spock intervention or sharing his mind.
I believe that's when he realized that Spock does care. If not for himself, he does so for Jim.
And that he doesn't want to make Jim feel bad for telling him, what he believes is right or wrong. But he wants to help him by being honest and open with Jim.
Also that Spock is right. Because hunting their villain like that isn't what starfleet isn't about. Nor is Jim. And when he turns to look at Spock, it's as if he just waits for his first to say anything. But Spock trusts Jim to do the right thing. This leads to Jim changing the mission and for the first time deciding for something Spock would do.
The thing is. Jim still doesn't know if it's right to do it this way. Also he probably thinks, that now he will lose captaincy for real, because he doesn't follow the instructions of Marcus.
Spock who seems to be aware of Jims inner conflict, comes to his side and tells him he would be happy to accompany him on the mission.
It's the first time Spock gives Jim the impression of staying by his side, even if they don't play after the rules. No complaints what they could do instead. Or what can go wrong.
You can see by the way Jim smiles, that he is for the first time since a long time relieved for having Spock by his side.
It's just a small and short scene.
But I think it weights a lot, because Spock here could have gone back to work. Or he could have taken the moment to settle things with Uhura.
He choosed Jim. And used his rhetoric especially for making Jim smile, because he knows how hurt his captain must be.
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