There's something they said on the commentary about Mary (whether you choose to believe the writers or not) - she's very like John and Sherlock in that she can't go for more than 6 months without an adventure.  (She certainly won't be left at home when John goes off on his adventure at the beginning of HLV, even if she doesn't have time to get dressed!).   So although it would be convenient to have Mary alive, providing childcare while John has adventures, it doesn't seem to fit with how the writers envisage the character.

There's also a slight issue in leaving a child alone with somebody who may be at risk (of being murdered).   Are they sure that killing Magnussen has made her safe? 

I don't think the team would work as a threesome, and I think that's another thing the writers have been clear about - that it's Sherlock and John's story.

Now that months and months have passed since the original post-- I'm curious what people think, now? Me, (as much as I don't like the idea) I think mary will stay and be part of the team for at least part of s4.

I reckon Mary wil stay, perhaps for the first episode, but they'll kill her off quite soon, because doing it in the final episode would be too cliched. And in the first episode, for the time she's there, she'll be in the 'background' in order for them to set up the premises for her demise and the whole drama around it  (eg someone coming after her, Moriarty doing something to her, etc).

I have always had a feeling that Mary isn't powerful enough now as a character to turn out to be a baddie. After shooting Sherlock, and with that terrifying stunt at the hospital with him and in the empty house - she had great potential. I was intrigued.

But then the whining about 'omg I love John' started, the crying about 'Mary Watson' started, and (at least in my eyes) she went back to being the usual female in distress character that had to be forgiven (as per Moffat's bueprint).

So, to me, there will now be no going back to 'evil' Mary. She's said her piece and we now know her intentions weren't 'evil' - she was just stomping her feet and panicking about losing her husband. It'd be almost comical to me if she turned around and started trying to pull the 'evil' face again.

You don't think Mary could fake those emotions?  Sherlock can cry at the drop of a deerstalker.  
I'm not saying this is how it will turn out but I still think it's totally plausable for Mary to be a real villian.

I think we as fans sometimes forget to remember that Mofttiss have to build the story on different levels - yes, they are building a story, but they also have to do so following the rules of storytelling - especially when writing for such a specific medium (TV). You need to keep the audience interested, but also you have to vary the tension and provide relief at times. So, in the way I saw it, the explanation we got from Sherlock in the Baker Street domestic is the one we are meant to accept - Mary didn't mean to kill him, hence why she shot him in the chest/abdomen and not in the head, and she saved him that way. Since he was a witness, had Mary been a different, less scrupulous criminal with no 'sentiment' for Sherlock she would have killed him and eliminated the threat that he was posing after seeing her - but she didn't, because she didn't want him dead.

Now. We, as the audience, are not meant to know all this beforehand of course - that goes against all the rules of good storytelling. We are instead meant to suffer with the protagonist, fear for his life, be confused just as he is on Mary's motives, and root for him to survive. So that's why they made him flatline at the hospital. That's a major point in the structure of the episode, and gave Moffat the chance to explore Sherlock's feelings and tell us something else about his background and relationships - as well as break our heart and make us suffer.

I think we tend to forget that the 'technical' aspects of storytelling are just as important as the 'content' of the actual story. We want to analyse everything by logic and cause-consequence chain. But imagine how it would have been if Moffat had made Mary say, "Wait, Sherlock - I have to shoot you, but don't worry I don't want you to die, I still care about you, it's just surgery". (Obviously this would have been a shit line to begin with , but let's pretend for the sake of the example).

The message at the end is exactly that, but Moffat had to crank up the tension to keep us interested and entertained. (And I think the mind palace scene while he flatlines was one of the best, most heart wrenching and most beautiful scenes I've seen in a TV show).

The feeling you have about the USB stick - I'm afraid that you are right. I am sure they will not go back to that. Why should they? They have explored 'Mary the killer' in HLV. Her character has done what she needed to do. John has burned the stick now - it's him drawing a line behind all of that. She is Mary Watson now.
Someone or something could come back to get her, but let's face it, for that to happen we don't need to know more about her background - we already know why someone could want her dead.

I think making Mary a villain again would be just a repetition, and I don't see any reason for them to do that. It's done, she made a mistake, she obviously has sentiments for John (and Sherlock) - she's now Mary Watson. Why should they go there again? Wouldn't that just be a repetition of her turning around in her  (silly) ninja outfit? We've had that already. They need to move on.

She won't be in the background, per se, but remember she is supposed to be pregnant now so someone has to look after that baby (if she is ever born) (zzzzzzzz).

I want to add that I am not a fan of Mary at all and I hope she goes quickly  -especially because I don't believe she has anything else to add at this point. And if the only reason Mofftiss made her pregnant was just to get her out of the way because she needs to look after the baby - well, I'll say it now - I WILL LITERALLY THROW MYSELF OUT OF A WINDOW.
 

I feel similar. I feel this would be too much of Dallas and alikes.
I feel Mary would have to take a bit of backseat and not show up too much. After S3 I would prefer not too much concentration on the Watsons relationship again and drama around Mary. I would prefer concentration on the boys and their work together.

Going by how they like to keep it in the family then Babybatch plays the part of baby Watson.

Gah, reading all those examples made me feel a bit queasy! And for me, there's no connection with the Sherlock being drunk thing or him showing a beheding to a child. Sherlock being drunk = a ONE OFF, unexpected, funny for a couple of minutes, but I wouldn't have liked it if it had been going on for longer than it has or if it had happened again. Archie = never saw the appeal, didn't care about him, not interested in seeing him again.

John lugging a baby on the crime scene and Lestrade rolling his eyes and complaining? NO. NO. I would definitely, definitely not interested in a show where John has to juggle a baby in order to do what he's supposed to (which is go on adventures with Sherlock) and baby/Mary/nappies/babysitter-Mrs Hudson jokes have to happen every time they need to explain what's happening with the baby (and they would need to, because they can't introduce a baby and then just ignore it as if it wasn't a huge part of John's life).

NO. God no. Sorry, just had a bit of an allergic reaction there!

John then returns to Afghanistan because, obviously, he has no further use in the story (except babysitting) now that Mary has been added as the new Sherlock´s assistant.