It's quite sudden, when he comes back. One day, John comes back from the shop round the corner, carton of milk in his hand, and there he was, sitting in his chair reading a newspaper. And John is shocked; completely, irrevocably shocked, to see this dead man alive in front of him, wearing that bloody purple shirt, his hair perfectly rumpled. And then he looks up, and spots John, standing there with his milk, and just smiles, folding the newspaper in half, "Ah, back already? Good, I needed more milk,"
And he just takes the milk, and bustles off to do God-knows-what. Just like that, he's back, no explanation, not even a 'thank you, John' for the milk. And they slip back into their old routines, John occasionally being woken up in the middle of the night by tiny explosions, or glass shattering, and Sherlock randomly throwing minor fits.
Mycroft is there some mornings, no matter the time; including one very memorable time, when John is on his way to the loo wearing nothing but a pair of red pants, and Mycroft greets him with a smirk on his face. John blushes beet red and hurriedly scampers off to the toilet to hide until Mycroft leaves, but not before Sherlock notices him and has a laugh with his older brother.
But he still doesn't know what happened when Sherlock fell, -he refuses to believe he jumped- and he only asks him once, but when Sherlock just continues to play his violin like he hadn't heard, he didn't ask again because he's scared of what the answer might be. And since Sherlock never brings it up, John is certain he will never know.
Sherlock surprises him one day, and brings it up, asking "Do you know why I did it?" and when John shakes his head, he just looks at him appraisingly for a few minutes. And then he kisses him, and John is so startled, he just kisses him back. Later, when they're lying in bed together, and John is dozing off, his eyes glassy, Sherlock wraps his long arms around him, pulling his back closer to his chest.
Despite his long, angular frame, he is quite adept at cuddling, and John smiles briefly, snuggling up against him, his eyes drifting closed. "I did it because of you," Sherlock murmurs, lightly kissing the top of his head before closing his own eyes and allowing himself to drift off into dreamland. John smiles contentedly, gripping Sherlock's arm briefly.