Oh, the feelings I have about this one, single moment in Young Sherlock. (Yap incoming)
In my opinion this is THE most important line in the show.
There is less than a minute left in the episode, and this is what everything has been leading up to -- and it is portrayed just beautifully by the actors.
From James, the long pause. The complete stillness in said pause. The unwavering eye contact. The little squint. As if he is deciding very carefully how he's going to proceed, even as he talks.
And Sherlock's reaction; he turns to look at James. Is he seeing him for the first time? This show has given us a Sherlock Holmes who has not once been afraid of sharing his true thoughts, of letting himself feel and act on his emotions, of getting close with the people that he chooses to and being fiercely protective of those he loves, of practically wearing his heart on his sleeve. And yet here, in this moment, after all the events of the season... his expression shows NOTHING. This is the most guarded and controlled we've seen him, after he has learned that sometimes the people closest to him cannot be trusted.
'Surely, by now, you know me.'
And Sherlock realises (along with we the viewers) that he doesn't. He doesn't! We don't know James at all!
We can count on one hand everything we can reasonably assume about James, and the list of things we know for certain is even shorter. We know that he is Irish. We know that he was at Oxford on a scholarship, and could not afford to pay for lodgings anywhere after losing said scholarship -- so, he is fairly poor, or at the very least doesn't have access to money. These are the things that we know for sure. He says that his father had a copy of The Art of War, and that it 'didn't do him much good' (whatever that means. It is, of course, intentionally vague on James' part). And he says that his mother died from consumption when he was very young. But that's it. And there isn't even any evidence to support what he says about his parents.
The thing about his mum in particular, he says this when he is trying to get something (to piss Sherlock off by warming up to Cordelia) (Which is another scene I have many thoughts about, but that's a whole other can of worms). He has an ulterior motive, and he uses a sob story to get there -- is he telling the truth? Or just what his goal calls for? Because we know so little about James, there is no way of knowing when he is being truthful.
And Sherlock knows this. As much as he doesn't want to admit it, he knows that James has a penchant for lying to get what he wants, that he is okay with using unconventional or downright cruel methods if it means he will get what he is after. And sure, sometimes this quality is noble and brave and caring, but sometimes it is selfish and cold. And Sherlock, unfortunately, as much as he wishes he didn't, knows this. And maybe he is realising that this is something about his new friend that he can no longer continue to ignore.
And in the aftermath of this whole... situation with Silas, Sherlock is not only realising how little he knows about James and the implications of that, but he is being confronted for the first time by just how much James knows about him.
James, who he has known for at most a couple of months, and at least a few weeks (the show timeline is vague). James, Sherlock's first friend, presumably the first person outside of his family to even say they could know him at all. James who has seen Sherlock bloodied and beaten and shot, who stood by him when he was arrested for murder (after having only known him for two days!), who learned about and took in his stride all of Sherlock's extensive family issues, who saw Sherlock's own mind deteriorate. His mind, that brilliant thing that Sherlock values above all else, James saw into it like no one else ever had. And Sherlock had been so caught up in how wonderful it was to have a friendship like his and James', that maybe he had neglected to see how dangerous it could be.
He has learned that people who know everything about him have the ability to use that against him. His own father -- someone he should be able to trust above anyone else -- used his knowledge of Sherlock against him, to lie and manipulate in just the right ways. He believed Silas, and let him get away with destroying his family and keeping them apart for all these years, because Silas knew him, and knew exactly how to get to him. And Sherlock feels guilty, but he is also ashamed, and I imagine he doesn't want to let this happen ever again.
He is realising, maybe, just how similar James is to his father. Just how similar their relationship is -- one who knows everything about the other, has seen him at his very worst... and the other who knows nothing about him. And he knows exactly where that led the last time.