I admit it is strange that we never see Mycroft and Mary together except in the farewell scene at the end where they do not interact at all. Which leads me to Sherlock's call to Mycroft. Why does he want to have him there? And why does Mycroft not want to come? 
On the other hand I cannot believe that Mycroft would plant a former assassin who has done things bad enough for her to be blackmailed by Magnussen so close to John. He knows John is his brother's best friend. Even if she had not shot Sherlock she would have been dangerous. 

And he would have researched her thoroughly.
If Mary has been planted there - which is entirely possible given her special "talents" and the fact that it would be an enormous coincidence that someone like her meets John just like that - I suppose it was by someone else. Which of course may depend on the question if Moriarty is really dead or if someone uses him. 

On the one hand I can't really believe that Mary and Mycroft are connected, especially not in a way that Mary works for Mycroft. But on the other hand there are some things that are really odd about Mary's secret assassin past. I mean, Mycroft is from the MI6 (!) and he had obviously kept an eye on John during Sherlock's abscence. Therefore I think, it would be logical for him to take a look at John's girlfriend respectively soon-to-be fiancee as she would be part of Sherlock's life as well as soon as he comes back. So, why hadn't Mycroft discovered at least that something is wrong with Mary? Sherlock unrevealed that Mary Morstan is a fake identity within a few hours after he escaped the hospital.
And then there is the shooting. Despite of all his sarcastic behaviour we still know Mycroft cares deeply for his little brother. But we saw almost nothing from Mycroft after Sherlock was shot. I expected him to be furious (just like Mummy Holmes ). And I can hardly believe that Mycroft would not be able to seek out the truth about what had happend in CAM's tower.

*sigh* This is all very odd and confusing and one of the many frustrating open issues HLV left us with.

I can't imagine Mycroft sent Mary in to look after John as that just seems too much, but do I like the idea of him knowing about Mary, just because he has his hands in everything. He doesn't really seem to have an interest in John's life outside of it being entangled with his brother's - he even indicates as much in TEH when debriefing Sherlock. 

My impression of Mary (and I may be way off base here) is while she may have formerly worked for another government's spy agency (say the CIA), she hadn't exactly left on the best terms, she had gone rogue or done something she shouldn't have. If she had worked for the CIA and was just in retirement, I doubt they would have abadoned her to forge a new identity on her own (Burn Notice's artistic liscense aside). When Magnussen said there were people who would want to know where she was, I took it to include her previous  government employer. I don't think Mycroft as part of MI6 would know about her and not do something about it, which leads me to think (at least before the shooting) he had no idea. 

However, after the shooting, Mycroft would realize as everyone else that Sherlock would have seen his attacker as he was shot in the front at such close range, and being observant, would notice John having moved back in, may have made a few deductions and uncovered some information in the wake. Obviously he allows her to spend Christmas with his family, so he's either concluded the same as Sherlock, or hasn't made the correct deduction yet. 

But Mycroft doesn't ask Sherlock why he goes after Magnussen. He asks Sherlock why he hates him. 

No, Mycroft said he was glad Sherlock stopped going after CAM. Whether he actually believed that is anyone's guess but under the hypothesis that he knew what Sherlock was up to, and knew that it was because of Mary, he could still be interested in the reasons why Sherlock hated him. 

I don't think Mycroft is to be credited for Mary Morstan coming into John's life. I guess she possibly was planted close to John by someone, though I don't think it was Mycroft.
What is odd though is how intimately Mycroft was informed about John Watson's life after Sherlock had left, right down to the point where he knew when John would be at a certain restaurant...
But I still think there isn't much of a connection between Mary and Mycroft.
Mycroft has always kept a close eye on John for Sherlock's sake, I guess, but I don't think this necessarily extends to his girlfriends. Seems like a bit of a splurge on intelligence personnel, which certainly could be better put to use otherwise, given how many girlfriends John must have had before he finally met Mary. Just remember the list Sherlock rattles off in A Scandal in Belgravia, if John kept going at that rate until he met Mary, oh dear...

It would be interesting to find out though, when Mycroft finally became aware of who Mary Morstan really is. I agree it's odd that he was never seen when Sherlock was in the hospital or at any point in the aftermath of him getting shot (except for in Sherlock's mind palace of course).

As for Magnussen wanting to get to Mycroft in the end, I think he knew that. People like Magnussen are always out hunting for the powerful, thus to gain even more power themselves, so Mycroft was pretty much top of his list. I'm certain Mycroft must have been clever enough to realise that.
 

silverblaze wrote:

Did I mention that Mycroft makes me paranoid?

 
LOL  , you are not the only one. I find the Sherlock/Mycroft christmas scene also very suspicious. Especially the "maybe it was something in the punch", Mycroft is far to clever to be tricked so easily  .

So he'd me more suspicious or less? 

Maybe it's all supposed to be taken on face value but, you know, Moffat...