I'd like to respond to
marsdaydream@Tumblr's list of the bitterest pills we were expected to swallow in season 3, especially His Last Vow which contained, for me, the most consistent characterization of them all.
Sherlock never realized who/what Mary is, because he wanted to like her. The "I want to like you" emotion made his abilities disappear in her presence.
Purely on a surface level, it would've been hard to dislike someone who took his side in the battle to get John to forgive him, let alone offered to put in a good word on his behalf. Especially seeing as she's the person who should've stood by John's decision to walk away no matter what.
Sherlock sets aside a lot of things he doesn’t have immediate answers to (most notably this season, who put John in the bonfire and why). Yes, he deduced that she was a liar on the first night, but Sherlock liking Mary wasn’t really about him - it was about the fact that John already liked her, rather a lot, and she gave him something that Sherlock can't: normalcy, which John has repeatedly expressed a desire for, even as he willingly set everything else aside when the game was on.
Coming between them wasn’t an option because even if John left her (before finding out she was pregnant), he’d have a hard time forgiving Sherlock for ending the (second) most significant relationship of his life. (Which would've seemed spiteful before the revelations of His Last Vow - just imagine how patently ridiculous Sherlock would've sounded saying, "I just know there is something suspicious about your fiance.")
And on a purely practical level, liking Mary gives him greater access to John.
Mycroft never realized who/what Mary is. (I guess the jury’s still out on this one.)
Jury is definitely still out. But he said he kept a cursory eye on John, which means that he likely never “kidnapped" Mary the way he did with John - and while surveillance, electronic or human, has its uses, if there seems to be no reason to dig further then why go to the effort of legwork? Then, after she shot Sherlock, Mycroft would have agreed to stand down at Sherlock’s request.
A trained assassin in hiding was okay with having the world’s most observant man sitting under her nose planning her wedding.
She had seven years to build a new life. Maybe she had help, either official (a witness protection sort of deal) or not (assassins don’t decide to get out of the game without a lot of favors to cash in with useful people). The people Sherlock would speak to knew nothing, and therefore had nothing to hide.
Sherlock did the right thing when he forgave Mary for killing him, because it was her only logical course of action.
Let's set aside that, strictly for plot purposes, Sherlock needs to live for Magnussen to get to Mycroft.
Sherlock said he didn’t believe she was trying to kill him, only buy time to negotiate his silence. No, science doesn’t quite allow you to shoot someone in the abdomen and guarantee anything but a slow, painful death of either perforated organs, internal bleeding or sepsis, but Sherlock called it surgery so I’m letting that stand. He recognized that there was no other way to keep the scene from being the end of her and John, so she did what she could to keep him from ruining everything on the spot. And forgiving Mary was never Sherlock’s choice to make - it was John’s, and he obviously struggled with it for six months.
But aside from all that, she didn't want to kill Sherlock because what she saw when she met John was just his grief; she knows now that being part of Sherlock's world makes John more alive in every respect. Of course she wasn't going to take that away from him.
Mary likes Sherlock, even though she didn’t trust him to help her, and even though she seemed willing to shoot him more than once.
Of course she does. By accepting Sherlock, she acknowledges what's already apparent: that to be happy, John needs not just Sherlock’s friendship but to remain part of his professional life. If she makes him feel welcome in their dynamic, it allows John to indulge his more dangerous impulses without resenting her for tying him down.
As for the shooting, great detective or not Sherlock couldn't be expected to deduce the logic of her actions, seeing as how she SHOT HIM. Her threat in the empty house made it clear that she intends to protect John - especially from her former life - at all costs.
It was totally noble and romantic of John to take Mary back after she’d lied to him from the beginning of their relationship, gotten pregnant and shot his best friend, because she’s worth it and deserves a new start in life.
John was never set up as a paragon of virtue, and "noble" is not how I'd characterize standing by the mother of your child. And I don’t think it had anything to with Mary deserving anything. It was about John deserving a normal life, happiness, a child and a partner (because as much as he and Sherlock are a matched pair, in John’s head Sherlock is larger than life, invincible and godlike) after everything he’s been through. Mary pulled him out of a dark place, maybe even darker than after Afghanistan, and he decided that his love for her, and his hope for the life they’ve built together, outweighs the life she led alone and left behind.
Sherlock Holmes and John Watson are not each other’s pressure points.
In John’s mind, Sherlock is superhuman. He doesn’t want to know how Sherlock faked his death because, like his deductions, the act is beautiful not for its details but for Sherlock having synthesized them into a cohesive whole. Sherlock is a magician, in his own way. But he is definitely not John Watson's weakness - Sherlock is his source of strength and hope in an otherwise mundane and unjust world.