It takes a couple of months after Sherlock comes back for them to get settled back into a pattern of sorts. They successfully cleared his name with the arrest of Sebastian Moran - one of Moriarty’s right hand men - and they quickly went back to normal - well as close to normal as they ever got.
John goes to work at the surgery, picks up groceries, and maybe some take-out on the way home, they eat together, and Sherlock rests his head in John’s lap while they watch telly. They go to bed, typically in Sherlock’s room, they wake up (sometimes when Lestrade calls) and John either goes to the surgery or off with Sherlock. It’s nice.
Their physical relationship hasn’t really been progressing, though. Not that John minds - not at all. He’s content with cuddling, frankly, because he’s doesn’t want kissing or sex from anyone but Sherlock, and if Sherlock doesn’t want those things, John really doesn’t care anymore. He tries not to think about it, really.
One case they’re on, the two of them split up to track two different suspects. John is wary, but Sherlock promises him that he’s not certain which of them is the culprit and he needs more data on both of them - quickly.
Lestrade calls him while he’s tailing his suspect, of course, and tells him that Sherlock’s been shot. He stops breathing for a moment - and then he’s in a cab on his way to the hospital. It takes a lot of convincing - and possibly some involvement from Mycroft, John really doesn’t want to know - for John to get to see Sherlock. He looks fine - he’s not even unconscious - apparently he was shot in the foot, and it didn’t hit anything important - the shrapnel was easy to remove, but how was John supposed to know? Especially when Sherlock sent him off on a wild chase again, knowing he was putting himself in more danger than John.
“You’re an idiot,” John says firmly, taking Sherlock’s hand and gripping it tightly.
Sherlock isn’t looking at him.
“I said that you are an absolute bloody idiot, and I would -”
“Do you know what word is most difficult to translate into English?”
“No, Sherlock, I don’t. Please explain to me how this is -”
“Ilunga. It’s a Bantu word that is very nearly equivalent to the idea that three transgressions become unforgivable - however, instead, it is the idea that the feelings change every time one is transgressed against - a transgression may be forgiven the first time, tolerated the second time, but never the third.”
John shakes his head. “What on Earth - what does that have to do with anything right now? You just got yourself shot, and I wasn’t even -”
“This is the third time, isn’t it? Three strikes?”
He sighs. “What?”
“This is the third time that I have tricked you and put myself in danger - first being the pool, when I also put you in danger, second being the incident at Bart’s, when I caused you years of grief, and now I’ve caused you even more worry and you probably owe Mycroft a favor for being able to get in here...” Sherlock keeps looking at the wall opposite him, never at John, and this is just completely ridiculous.
He puts a hand on Sherlock’s face, forcing him to make eye contact. “I’ll repeat myself - even though I know you hate it - for a genius, you really are an idiot. If I actually counted all the things you’ve done to upset me and cause me worry, I would have left a long time ago -”
Sherlock swallows, and continues to shift his eyes nervously. “John, I -”
“But I don’t care. I don’t care how many daft things you do, because I love you, you prick, and I’ve already told you that, and I am not going to leave or let you leave just because of the stupid things you’ve done now and again. You’re brilliant, and my life was lonely and frankly, terrible without you, and I will not choose to go back to that.” He smiles, then, as Sherlock finally meets his eyes. “Also, on that note, if you try to protect me by putting yourself in danger again, and you get hurt or I think for even a moment that you are dead, I will kill you myself. Understand?”
Smirking a little, Sherlock nods. “Yes, John. I understand.”
John nods back and tries to move away a little, but Sherlock brings up a hand and puts it in his hair to keep him from pulling back. They sit there for a moment, breathing each other’s air, and John has to close his eyes, leaning their foreheads together. When he finally gives in and presses a kiss to Sherlock’s lips, he doesn’t pull away, but John still keeps it relatively chaste before he pulls away - and he can still feel his blood fluttering in his veins.
“I’ll always forgive you, just... please try not to make it so I have to quite so often?”
He feels Sherlock nod, as he keeps his eyes closed, and neither of them pulls away until Sherlock hears the doctor walking down the hallway.