Yes, I think John/Mary endgame is impossible. No, I don’t think Mary is necessarily a bad guy. I think people are really jumping the gun if they automatically assume that’s the case.
I know lots of people hate Mary, and hope it turns out she’s a bad guy. And lots of people adore Mary, and hope it turns out that she’s on John’s side. But hope is not a valid predictor for what the show will actually do.
Look, there are three actual possibilities here, and possibility #3 gets overlooked a lot.
#1: Mary is being honest with John now. She loves him, and she’s on his side.
#2: Mary is actually the last bastion of Moriarty’s organization and is going to double-cross them and horrible things will go down.
#3: Mary is lying about or hiding something else non-Moriarty-related.
I can tell you what they’re not going to do in a million years: they’re not going to say, “Whoops, show’s over, John can’t go out to play anymore” or have Sherlock go out and buy a replacement sidekick. People seem to be afraid of this, somehow, but come on, it’s just ridiculous. That’s just not how television works.
But something bad is going to go down. It needs to! So far, this show has not demonstrated itself to be a show where the good guys die. Bad guys certainly do. And sometimes victims do. But our main circle of characters? Heck, Sherlock and Irene have both come back from the dead. Our named cast of characters is looking pretty impervious at this point.
And there’s the rub.
At this point, if I were writing this series, I’d be feeling that. I’d be saying to myself, “Man, this show is starting to play like a cartoon. We need to show our heroes can’t always win without paying some kind of cost. We need to make them bleed, here.”
In terms of keeping the show running, Sherlock and John are not expendable. But everybody else is. And I think we all have the sense that, somehow or other, it’s going to come down on Mary. She did, after all, die in the original canon.
Honestly S3 does make more sense if it turns out Mary is actually a double agent and the last remnant of Moriarty’s organization. Plotwise, it’s the most diabolical thing she could possibly be. In fact, it puts her in the position of being the most effective villain I think any version of Sherlock Holmes has ever faced. Because if this is actually the case, it means she’s already won. Even if (well, when) they discovered her and took her out, the emotional damage she’d leave in her wake would be an effective revenge.
But. Personally, while I think Mofftiss are clever enough to do that, based on their past history I don’t see any reason to believe that they are indeed going for the double fake-out with her. This is not a speed-chess style series like Mission: Impossible or Leverage, where spectacular sudden revelations abruptly reconfigure the entire board. (At least, so far it hasn’t been, but then again now Sherlock is working for MI6 and John’s married to an international spy, so who knows?)
Furthermore, I don’t believe that the argument that ‘It would make the season make more sense’ is worth much as evidence, because realistically, Sherlock’s cases have never made as much sense as people like to tell themselves they do. The Holmes cases in any permutation have always been a bit shaky if you think too hard about the details.
So in balance, I think it’s probably somewhat more likely that Mary is on the up-and-up. But the problem is that if this is true, then it leaves us in an awkward position, story-wise. Mary is clearly crazy and dangerous enough to fit right in when it comes to the cases. Whether she joins in or sits out, she can hold her own, and hell, the cold truth is that she’d be more useful on a case than John, in a lot of ways.
But let’s think about this a bit more. Sherlock is famous. He gets into the newspapers and on TV. John gets there with him. You think that if they go down this road, Mary won’t ever get mentioned? That at some point her photograph won’t end up in the Daily Standard or something? And that then millions of people will see her face, probably including one or more people who would like to see her dead?
And then, what about the baby?
John’s pretty messed up, but do we see him as the kind of parent so irresponsible that he’d continue throwing himself into risk of life and limb on a weekly basis when he’s got a kid at home who needs him? Even worse, John has been used successfully as leverage against Sherlock several now, and now Mary has. John has to be considering how that baby could threatened or taken hostage against him or Sherlock or Mary. (Doesn’t he? Oh god, I hope he is.)
So if Mary is being honest, then the situation as it stands is not sustainable. Something is going to happen to that kid. Maybe it’ll turn out not to be John’s, or maybe Mary will miscarry, or…something, because the work they would have to put into navigating around John having a baby would just get too extreme for a show that only has three episodes every two years to reasonably sustain.
Of course there’s always that #3 I listed up there: that she doesn’t work for Moriarty, but she’s hiding something else. I mean good god, we know she is. She’s flat-out told them that she’s got an entire lifetime of enemies and shady secrets. They could probably keep the show running in perpetuity just on the strength of the BS she brings to their door every month. Basically, if they want to go the route of Mary’s past coming back to haunt her, anything could happen in S4.