Perhaps one of my favorite tropes is when John unexpectedly becomes a father (and, therefore, Sherlock becomes one as well). There is a lot of Parentlock out there but within that genre is a small subset of these stories where John’s previously unknown children just show up at his doorstep or he stumbles across them on an investigation.
Perhaps my absolute favorite of these is The Sound of Silence by Cloud_Wolfbane. In it, we meet Hal, a small five year old mute, who is rescued from a foster home from Hell, where he is abused by his NotMother, to whom he loses his voice to, and where his curiosity and need to learn is fostered by the older boys in the house, who trade him food and leftover school supplies for him to do their homework and chores for them. It is so sad to think of this small boy kept like this but then he is pulled from it all and is taken in by our two favorite detectives. Soon after, we find out that Hal is actually John’s son from a mistake of a night and from there John and Sherlock take on the challenge of raising this exceptionally bright boy. It is such a great story and filled with plot twists and spots that make your heart twinge, like the first time Sally meets him or the first time he speaks. You can find it here: http://archiveofourown.org/works/860533/chapters/1648837
Cloud_Wolfbane is also the author of another great story called A Twist of Fate. In this one, Sherlock is an Omega who forgets to take his suppressants one night when is is coked out of his mind. He ends up spending the night with a Scottish Doctor who is being deployed the next morning, of whom he never finds out his name. The next morning the doctor is gone and Sherlock is pregnant. Miraculously, he and the child survive the pregnancy and thus comes Hamish into the world. Time passes, Hamish being exceptionally bright and hopes to become a consulting diagnostician instead of detective. While working on a project, he employs the help of a doctor he meets in passing at Bart’s named John. Little does he or John know that they are more deeply connected than they could ever imagine and it is up to Sherlock to give them the key to a future of together. I know some people aren’t up for MPreg or Omega/Alpha dynamics but if your are up for it, it is a very good story and can be found here: http://archiveofourown.org/works/838518/chapters/1597745
Another really sweet one is called Danny by TheWalrusAndThePenguin. In this one, after just launching into a relationship with Sherlock, John finds out a woman he was in a relationship with has died and unknown to John had his son, who is named Danny. John takes the boy in and he and Sherlock begin to raise him. It starts to weigh on their relationship and John leaves. Sherlock doesn’t do well without his family and begins taking on more and more cases. One leads him on a fateful trip to Switzerland and we all can imagine what happens from there. This one is sweet with a rough and tumble little two year old with blond curly hair who finds a place in both their hearts. It gives you a great glimpse into the domesticity of 221B but also wrenches at your heart when they each lose their family in their own ways. You can find it here: http://www.fanfiction.net/s/7793991/1/Danny
The fourth of a series of stories featuring 3Cs Watson’s unknown children comes to us in the form of a stroppy teenager named Jocelyn Jayne Morstan, which people to seem to use her full name a lot so you just have to get used to that if you read this WIP called And Then There were Three by Grovehove. Now, if you like none stop action, lots of teenage angst, humor and embarrassment (I don’t think I would want to talk about my time of the month with Sherlock either) then this is the story for you. It is also filled with a lot of heart and three people orbiting around each other who eventually pull together into the best of families. This one you definitely need to check out. You can find it here: http://archiveofourown.org/works/528902?view_full_work=true.
Occasionally, though, John isn’t the father but is the parent the child needs. Perhaps the best of these is a story called Too Much to Hold by Sparkle_Free. In it, John finds out two of his friends from Uni have passed away and have left him their autistic son, Julian. John reals at trying to be the right guardian/father to this poor child, who has lost his family and has come to 221B in refuge. Soon, John finds out that his greatest asset might be his best friend and lover, Sherlock Holmes, who despite his best efforts soon comes out as autistic and very knowledgable about what Julian needs. But can John move past any jealous or tentativeness he might feel about the bond that builds between Sherlock and Julian? Can he come back from the fall out from the major faux pas he commits while at a crime scene? Can he be the father he needs to be and the lover he wants to be to these two people who mean so much to him? All the answers are there and there is a case to boot that needs to get solved, so check it out. Especially for the moments between Sherlock and Julian, which are unexpected and precious, and the tightrope that John seems to walk as his and Sherlock’s relationship definitely swings left and right but eventually steads to where you want it to be. This is one I have read a few times and really is one of the absolute best Sherlock fics I’ve read. You should read it and can find it here: http://archiveofourown.org/works/270454?view_full_work=true
P.S. - sorry for the delay in this post. RL got in the way and likely will again this week. I promise, even if I miss a week to still post at least 52 weeks worth of stories. Sorry about that.