A lot of people I follow on Tumbler, LJ etc seem to be either baffled or upset about the fact that Series 4 of Sherlock may include not only Mary but also the Watsons' baby and feel that this is somehow going to change the dynamic of the show completely, and we're going to have nothing but Parent!Lock etc. I think what Series 3 and His Last Vow in particular showed very well is that Moffat and Gatiss like taking the formal outlines of an ACD story and then twisting the meaning of it substantially by updating the background. With that and the knowledge that they've already planned both Series 4 and Series 5, this is my speculation as to what they might possibly be going to do.
I start with the assumption that they're not going to kill either Mary or the baby off in childbirth. Given how pregnant she's supposed to be by the end of His Last Vow (probably about 8 months if the wedding was in May) and even allowing for the writers' completely hopeless chronology, I don't think that leaves them sufficient time to get enough drama out of her character after the big revelations of His Last Vow. On the other hand, I'm pretty certain that Mary is eventually going to be killed off, because she is in ACD. As to what they're going to do meanwhile, I want to go back to the start of one of the lesser known ACD stories: The Boscombe Valley Mystery
We were seated at breakfast one morning, my wife and I, when the maid brought in a telegram. It was from Sherlock Holmes and ran in this way:
Have you a couple of days to spare? Have just been wired for from the west of England in connection with Boscombe Valley tragedy. Shall be glad if you will come with me. Air and scenery perfect. Leave Paddington by the 11:15.
“What do you say, dear?” said my wife, looking across at me. “Will you go?”
“I really don’t know what to say. I have a fairly long list at present.”
“Oh, Anstruther would do your work for you. You have been looking a little pale lately. I think that the change would do you good, and you are always so interested in Mr. Sherlock Holmes’s cases.”
“I should be ungrateful if I were not, seeing what I gained through one of them,” I answered. “But if I am to go, I must pack at once, for I have only half an hour.”
There you have a picture of the ideal detective's companion's wife in Victorian times. ACD Mary not only doesn't resent Holmes' call on her husband's time, she actively supports it. The question is, how do you update such a dynamic to the twenty-first century without either making Mary look a complete doormat or John seem a negligent husband?
One ingenious answer is that you have Mary
as grateful to Sherlock. What John has ended up with is a wife who, given her back story, cannot justifiably complain about anything John or Sherlock get up to henceforward. Mary also knows that John needs to run into danger periodically if he's not to start his version of "looking a little pale", but she isn't going to come along with him for his adventures now for two reasons. One is because she's given her old life up and the other is because she's got the baby to look after. Even she probably realises that storming a crack den while breastfeeding is not recommended.
I think Series 3 sets up Mrs Holmes as a possible role model for Mary: a woman who was brilliant at her original career, but who has chosen to do something different with her life and stay at home with her children. I think it's quite feasible that Mary will in fact go back to working as a nurse after the baby, especially since she's conveniently already in a part-time job. But she's through with being a spy/assassin. Will she find being a doctor's wife boring? At times, but it's a decision she's chosen to make: she can't complain about it. And what will make it easier is that John, in time, will probably manage to romanticise her past life in his own mind (as Mr Holmes does with Mrs Holmes). John will admire Mary for her bravery, resourcefulness and shooting skills and forget the murky details of her past crimes.
So I think it's quite possible that in Series 4 we will get John and Sherlock off solving crimes while Mary stays at home with Baby Watson. I think we'll also have a few scenes of hopeless/wonderful New Dad!John and Uncle!Sherlock and possibly Mary coming up with one or two useful suggestions for cases (as Sarah did in The Blind Banker
). But she'll probably be mostly on the sidelines in a way that seems vaguely plausible. And then I think that she'll get killed off in Series 5, when we've got used to her, so we can have some more grieving John.
What about Baby Watson at that point, or rather toddler/young child Watson, if they're keeping very roughly to real-time chronology? A lot of fanfics seem to assume that John Watson would be the world's most devoted dad, but I see absolutely no sign of that in canon. BBC!Watson is a man who, when Sherlock has just drugged his pregnant wife, doesn't feel he has to stay with her to ensure their unborn child's OK. Instead, he chooses to go off with Sherlock on a mission that may end up with them both dead or in prison. In other words, John's priorities are still massively skewed towards adventure and away from domesticity.
So what I think will happen is that if Mary dies, those around John will realise that he's just not single parent material. There's no obvious family to take over. Mary is an "orphan"; one or both of John's parents are presumably alive but he's not close to them (and they may be elderly). Harry isn't suitable to rear a child. What I think might therefore plausibly happen in such a situation is that one of John's friends will make an informal offer to bring up/be the main caregiver for Miss Watson. The obvious person to do this would be Molly (with or without Greg's assistance). That would allow John to move back into Baker Street, but still see his daughter frequently, without having to worry about childcare if he needs to rush off with Sherlock to the West Country to help find a stolen racehorse. It also allows the writers to have some comic John and Sherlock plus adorable child scenes without either making John and Sherlock into an official couple or showing them as hopelessly negligent.
Anyhow, those are my guesses and I'm sticking to them – until someone comes up with a better hypothesis in the comments. Fire away!