If I'm going to complain and worry about the way slash writers treat Mary like I did in my recent post, I should be just as quick to highlight people who do it right. Case in point:
Luminosity by what_alchemy
In this story John shows up on 221B one night, baby in tow, and they become a regular fixture in Sherlock's lives. Featuring Sherlock as reluctant uncle, babysitter (he's really much better than you'd expect, but oh so convincingly so!), and in the face of various legal struggles coming from his lack of official guardianship, BAMF-in-need-of-bail. The only time Mary is even mentioned is at the very end, and even there it's almost incidental.
What makes this work so well is that Mary is not demonized. Neither John nor Sherlock dwell on how his marriage broke down, though given the events and revelation of HLV (and, let's be honest, the way Watson avoids Mary's past rather than facing it), the odds were never exactly in the favor of this marriage surviving much past a year or two, if they made it that year. But Mary is not blasted. Hers and John's divorce is simply a Fact, as is the part that she signed away her maternal rights. I can see this being a loving act on Mary's part, really; if she couldn't provide a stable home-life because of her chosen profession and personality, if she didn't and couldn't have friends and families to help support her with the childraising thing, if she saw that John had all of that through Sherlock and Mrs. Hudson, if she trusted John to do right by her child, if the divorce happened early enough in Mina's infancy... I can see this being the kind of decision that a loving mother might make and that isn't at all neglectful.
It's also treated as something Mary chooses freely. She is shown respect and dignity, even if she isn't involved in the story much at all. So this is pretty well an example of what I harshly called annihilation (Mary is more or less completely removed from the picture), but it's done in such a way that Mary doesn't come off as cruel or evil... just not there, for reasons that could be unjustified but that also could be completely justified. I can easily imagine Mary having a fulfilling life, hopefully one with a minimum of body bags. That side of things isn't what what-alchemy seems to be telling, but it's not told in a way that portrays Mary with a fair measure of grace and sympathy, or at least gives the reader the freedom to see the story in that light.
This story really isn't about Mary, though. It's more about John and Sherlock and Mina forming a familial unit together. And it's so charming! Sherlock's discomfort around a child, Mina gnawing on microscope eye pieces and Sherlock using technical linguistic terminology describing her and that whole exchange with Mycroft at the end and... yeah. Entirely too much to absolutely melt over in this short fic. I also love the fact that the functional family comes first and that any romance, which is truly G-rated, comes organically out of that. Sherlock truly loves John and Mina, love that starts out as friendship but bleeds into agape love over the course of the story. Romance, such as it is, is the natural outgrowth of this rather than the driving force.
And speaking as a fan of the Johnlock genre who has enjoyed her share of stories where the romantic love comes first? That was one of the most beautiful paths to love of any sort that I've read in a long while. This story left me smiling and feeling all warm inside. Do check it out.