just-sort-of-happened:

Why Mary Stands There

In the Baker St confrontation Mary immediately goes to stand next to the mantel.  Why?  Because there’s an open knife there.  She is ready for a fight and is not just armed with a gun but is also aware of this other weapon in the flat.  By standing to the left of the knife, she can easily grab it with her right hand and she can also prevent John and Sherlock from grabbing it to use against her.

Things that occur earlier in this episode enforce this idea.  Bill pulls a knife on John and John takes it from him, even asking if the knife is, ‘a clue’.  Here, with Mary, it most certainly is,

Only slightly earlier we get the idea of making do with whatever weapon you can find, here,

(*cough* pay no attention to the fact that Mary seems to be mocking his wang, here…)

Then, at Baker St, itself, we will have Magnussen’s henchman reveal that John has multiple weapons, 

(*ahem* pay no attention to the fact that Sherlock looks impressed as crap by John’s, ‘wang’, here, in stark contrast to Mary’s reaction…)

And soon after, Sherlock will mock him for it,

Except, there’s a clause, 

Now, that we know, ‘how the night’, went, we must wonder, is John armed during the Baker St confrontation?

In this nifty visual, we see Mary in relation to the knife and to John: she is a threat to him, but she’s looking away.  Maybe she doesn’t want to have to hurt him?

Ditto, here, with Sherlock, except she looks right at him in a penetrating way.  Maybe Sherlock she doesn’t mind hurting so much.  I mean, she did just shoot him,

With bonus: as Sherlock sits down, we see a sliver of Mary’s arm and the knife is seen as being right in his back.  She stabbed him in the back once and she would/will do it again,

Now, for poetic flare, let us harken to the sweet, sweet past of ASiP and see that this is a knife that Sherlock put here, on the mantel, the first time John walked into Baker St,

This is the knife he puts there because he’s, ‘straightening up’, for John.  He is trying to make his flat more appealing while also using a suggestive idiom for cleaning up.  Sherlock will do whatever it takes to have John in his life, including hiding his feelings and appearing straight.

This is the same knife that Mary will put in his back.  She is using his love of John against him.  She knows that he has a blindspot for her because he loves John and she has, up to this point, exploited this to her advantage, nearly killing him.