Everyone knows that Sherlock plays the violin. They don't know that he's rarely playing it for his own enjoyment, like normal people would; more often it's to annoy Mycroft or keep the neighbors up or work through a puzzle in his head. He very, very rarely plays the violin for any other reason, and most of the time what he's playing is crazed and frightening and really not meant to be enjoyed. But every once in a while, John will come home to hear actual melody coming from the flat. And he'll just stop on the stairs, listening, basking in it really. Too soon, Sherlock will figure out someone's listening, will stop or shriek into something awful. So for the short time he has, John closes his eyes and listens.
And, honestly, it's not that Sherlock is phenomenally, supernaturally perfect at the violin - not the way he is at everything that doesn't require tact. His playing is good, quite good, but he is not an utter prodigy at it. If John was to think about it any harder, he'd probably say that Sherlock avoids playing anything pleasing because his expectations for himself won't ever match his actual ability. Short version: Sherlock doesn't play the violin for pleasure because he is angry at his own lack of perfection.
Sherlock probably assumes, as most people do and he does about most people, that John doesn't know enough about music to know the difference between good and great. That's the only reason he can think of for why sometimes Sherlock lets him hear it. Sometimes John is allowed to catch a tiny snatch of beauty as Sherlock transitions from one angry atonal shriek to another. Sometimes Sherlock plays quietly at night, when he knows John is still awake. Sometimes Sherlock doesn't stop playing until he hears John's keys rattling in the door, never mind that he's known John's been there for long minutes. He probably thinks John can't tell the difference, won't notice anyway; or would think that Sherlock was a virtuoso and idolize him a little more for it.
Joke's on him, though, because if Sherlock thought about it he'd probably realize: John's a crack shot, a very good surgeon, a quick typist, sketches well and quickly, handy with repairs to appliances and clothing and furniture. If it requires precision and speed and a steady hand, he can do it, not perfectly but well, better than most people would expect. John knows Sherlock is frustrated at his own imperfection with the violin, and John knows who and what he's doing when music is involved, always. John can play. Not perfectly, not even as well as Sherlock - at least, not on things with bows, which always irritate a twinge in his wrist for some reason, probably his short arms getting achy at the angle. But where Sherlock only plays the one thing, John can play almost anything.
And so John decides, one day when he hears Sherlock torturing himself with a complicated bit of Bach, to pick up music again. He has a brief, highly amusing vision of them playing in a dive bar, piano (or guitar, or trombone, or clarinet, or any of the other several instruments John is proficient in) and violin, getting paid in beer and applause. So he starts ducking into music shops when Sherlock's not around. A decent used guitar is easy enough to find, and the trombone he buys off a schoolkid who's more than happy to stop playing, which is probably unethical somehow but he doesn't really care enough to think about it. The others he holds off on, for the moment, and instead keeps searching for what he really wants.
And the next week, when Sherlock comes home late from god knows what, it's John he hears playing; John's tastes run more to the popular than the classical, and he's happily plunking away on a small upright piano he found at some tiny shop somewhere, playing an execrable current hit with a melodic hook that makes Sherlock want to throw something or kiss him or dance, or perhaps a blend of all three. When Sherlock makes a noise (he's not sure what the noise was, only that it left his throat and was apparently audible) John glances back over his shoulder. "Ah, love, you're here." Turns back to the keys. "I'm having a bit of trouble with the 'Spring' sonata, thought you'd like to help me muddle through it."
A long, tense pause. Sherlock isn't sure how to react: cycles through possibilities, ranging from pulling John onto the couch and fucking him senseless to storming out without a word. He chooses something else, something he thinks will make John happy enough; goes and gets his violin, takes off his overcoat, finds a spot to stand where he can see John's face and hands. He's had the "Spring" sonata memorized since childhood, hates to play it because it is dependent on a good pianist, but John, despite his obvious lack of recent practice, is a good pianist.
They play, and it's like sex through sound - not because it's sexy as hell to watch John's strong, sure hands press keys and his eyes tense as he pushes himself to the absolute limits of his own ability, and to see Sherlock's long, lean fingers arch into the bow and clench around the neck - because they're in sync, they match well. Their styles mesh in interesting patterns: Sherlock soaks in the fact John's style is more obviously informal, obviously learned in churches and bars and shitty public school classes instead of in private lessons. And John, enjoying himself immensely, pokes and prods at Sherlock's playing, making him jump and keep it lively, not letting him rest easy on his own skill.
John's the more emotional player, obviously, but having stiff hands from lack of recent use plus having to actually look at the sheet music make him the lesser partner in the sonata, which gives Sherlock a perverse sense of joy in the playing. They finish the sonata and keep going, playing things they both know, not competing or pushing or fighting, just enjoying it, not really talking or stopping, and the music swells and fills the flat, trickling out into the night sky.