this will never hurt less than it does right now
Sherlock is still in the flat when John comes in.
He hears the door open and assumes it's Mrs. Hudson, but then a familiar limp clomps up the stairs, Sherlock hears the rustle of plastic bags, the clink of jars, and John's swear under his breath as he realizes he needs to get his keys out again because he's locked the damn door. When it opens, Sherlock is frozen in front of the window, and John drops the groceries.
He hadn't meant to be still inside the flat, he just lost track of time looking for what he needed, something he was sure he left in the flat, got sloppy, which is so uncharacteristically him that he thinks perhaps he meant to stay too long, but he's not one for psychology, so he'll think on that later. It's not the first time he's come back to the flat since faking his death, but it's most certainly the only time he's been caught.
Right now, though, right now Sherlock has to deal with the aftermath of what happened three years ago, how he jumped off a building right in front of John's eyes, how he watched John in the cemetery that day, saw him straighten his back and about face, turning right back into Captain John Watson.
Sherlock doesn't like to think about that day in the cemetery, because it would have been so easy for him to give John what he wanted, what he needed, and just shown himself. He could have saved them both quite a bit of pain. But he didn't, and the ache in his chest is a clear indicator.
He's been dreading this day for three years, and for a moment he sees hope flash through John's eyes, so intense and brief that it makes his breath catch. He opens his mouth to speak, but John beats him.
"Sherlock?" It's a whisper, raspy as if John is about to cry or as if he hasn't said anything in quite awhile. Both are logical deductions.
"It would seem so," Sherlock answers just as quietly, his voice low, looking just over John's shoulder. John moves toward him quickly, the look on his face has changed from hope to something much deeper that Sherlock doesn't have time to place before John's fist connects squarely with his jaw, knocking him backwards.
John grabs the lapels of Sherlock's jacket while he's hunched, and Sherlock doesn't even have time to ask what's going on-- because really, this is not what he expected, and he's played this scenario out in his head hundreds of times-- before John's mouth is on his and they're kissing.
It's not a sweet kiss or gentle, by any means, but it's careful in the way that John is always careful and full of emotion, years and years of pent up emotion, the way that John is full of emotions in so many ways that Sherlock doesn't understand but Sherlock can feel the emotions coming from him-- grief, relief, frustration, anger-- and he thinks that he finally understands.
John's hands are still holding onto his lapels and Sherlock's long fingers have slid their way into John's hair without his knowledge, and he realizes that he's kissing back, reciprocating feelings that he never knew he had. Sherlock thinks he feels a hint of teeth on his lower lip before John pulls away, breathing hard, hands still curled into fabric.
They stare at each other for a long time, and gradually, John accepts the fact that Sherlock is real, that he is not going anywhere for the time being and he lets go, leaving the fabric of Sherlock's coat terrifically rumpled. Not that Sherlock cares.
"I take it you missed me, then?" Sherlock asks, quirking an eyebrow, because this is all he knows how to do. He doesn't know how to say, I'm sorry I made you believe I was dead or I'm sorry you had to see that or You are the only person I would call before dying.
John scoffs and shoves him lightly, snapping the tension between them and then they're laughing and John is going to gather his dropped groceries.