John has seen past Sherlock's facade
So I’m wondering if someone hasn’t already written this, because it seems like fairly obvious stuff, but I just worked out the whole thing step by step in my head (it was a slow morning at work) and I wanted to set it down somewhere.
This might be worth writing out in more detail later, with actual quotes and stuff, but I’m pressed for time right now so it’s pretty much just off the top of my head.
In TAB, the question John is asking about Sherlock has changed suddenly. The entire rest of the show, John is asking himself, is Sherlock a sociopath, does he have feelings the way other people do. In ASiB, he tells Mycroft that Sherlock “doesn’t feel things that way”. In THoB, Sherlock has an emotional breakdown in front of John at the Inn, and John basically just denies what he’s seeing and refuses to take Sherlock’s emotions seriously. In TRF, John falls for it when Sherlock claims he doesn’t care if Mrs Hudson has been shot and calls him a machine.
After Sherlock returns we don’t see John questioning whether Sherlock has feelings so much but I think that’s really because between Sherlock playing dead for two years and his engagement to someone else he’s managed to put a little emotional distance between them. He’s telling himself it doesn’t matter to him if Sherlock can’t feel things the way he does, he’ll take whatever relationship with him he can have and try not to need him that way anymore. But there’s no evidence that John has seen the real Sherlock - except that he should have. At the wedding, during the best man speech. But we don’t KNOW.
In HLV their relationship is really strained and also I think John is having to hide things because he has to keep his emotions hidden from Mary so it’s difficult to tell what he’s thinking. But then we get to TAB, and suddenly John is asking an entirely different question. Not “do you feel things that way” but “why do you hide the truth of who you are.” John refers to his role as an unreliable narrator repeatedly, he talks about the version of Sherlock that he’s presenting to he world as distinct from Sherlock’s true self. When they talk at the greenhouse, he says he knows Sherlock is flesh and blood, that he MUST have a past, he MUST have impulses.
So John has changed from asking “do you have feelings?” To “why do you hide yourself?” In TAB, he’s seen past Sherlock’s exterior finally. But how do we know if this is true in the real world or if it’s just Sherlock’s wishful thinking?
Well, we don’t have anything from the episodes prior to this, like I said. But LOOK AT HOW Sherlock thinks of John in TAB. John is extremely perceptive and sees through facades. He sees that Molly is really a woman when Sherlock can’t. He understands that he’s just a character in a made-up-story. And Sherlock thinks he’s “pretty damn smart.”
So when Sherlock thinks that John has finally seen through to who he really is - I think this is actually what has happened. John knows, and Sherlock knows that he knows. They just haven’t had a chance to have a conversation yet.