John had stopped thinking too much about Sherlock's -how should he put this?- "eccentricities" a long time ago. When he had first moved in with the man he had been confused, and concerned about his lifestyle (heads in the fridge was not exactly normal), as well as creeped out, but over time he just accepted it as Sherlock being Sherlock, and stopped questioning those kind of things.
And when the man jumped, he took all of those things with him, and John found that they had not only been apart of Sherlock but him as well. He had tried to stay out of the flat at first thinking it would be just too painful to go back, but after the first week he realized that he had to go back, he had to. It was there home, his home, there life was there, and even if it hurt him to remember it he couldn't abandon it.
After that he had refused to move anything of sherlock, none of the experiments were thrown away, and he didn't even wash the last plate Sherlock ate off of. But it was all a hopeless game he was playing, and when he walked downstairs one morning to find that one of Sherlock's experiments had grown to contaminate the entire fridge, he but on goggles, a mask, and the rubber yellow glove he kept under the skin, and got to work.
He spent a solid six days doing nothing else but cleaning the place up, four and a half of which were spent just in the kitchen, then another week tidying the place up. He didn't get rid of any of his things though, and he had every right not to, they were his, Sherlock had given him everything. So he brought a filing cabinet and started to go threw all of his papers and organized all of them.
So one month after the fall, he called Sarah to tell her that he was able to start up work once more, and the next day was helping patients with a smile on his face. He was far from better though, he was able to trick everyone, even Mrs. Hudson, into believing that he had gotten over Sherlock's death, well everyone besides Mycroft.
Mycroft was still an insufferable bastard, and came to see him still at least once a week. At first it had been more than that though, you would have thought that the man he was most infuriated with, the one he blamed for his pain to give him some space, but no. The first week he did, but after he had moved back into Baker street, he came every other day, and the days he didn't it was either molly, or lestrade, and was always to be sure to be around the corner, at every single god damn moment.
He knew why they kept coming to see him, thought he may try to join his friend, but not once had John ever considered suicide. Maybe he enjoyed putting himself into situations where there was a high chance of getting hurt (he had lived with Sherlock for gods sake), but he was very against suicide. Not that he had never considered it before, before he met Sherlock and all he had was a god damn cane and the browning in his desk, but then Sherlock saved him and there was no way he was going to throw away the life he gave back to him. Yes it hurt seeing his things everywhere, seeing the people he had met through him, but they all where his family, he cared for every single one of them, and he wouldn't leave them.
He even ended up forgiving Mycroft. After two weeks of Mycroft constantly coming to see him (and following him, he wasn't stupid he knew that there were guards posted around), he had snapped, and much to his surprise so did Mycroft. John had started yelling at him, screaming, blaming everything on him, rating things that made no sense, and then cool stoic Mycroft was joining him. And after fifteen minutes of both of them going at it they just stopped, the flat silent besides their panting.
John had been about to go at it again, but had looked at Mycroft and seen, truly seen him. He was a man, just like himself, and he had just lost his brother whom he did love, and he was the reason for it, he was the cause for his brother dying and the guilt was eating him up. So then without thinking, he just walked over to the man, who stiffened at his approach like he was accepting a hit, and the fact that he looked like he was going to take it without a fight just convinced John further that it was useless to continue blaming him.
So he hugged him, true it was awkward at first, Mycroft had gone so still under him, it felt like he was hugging a statue. But when he had been about to pull away, he heard the umbrella drop and hesitant hands on his back. They stood there for a few more moments, and Mycroft rested his head on Johns shoulder, neither of them cried or spoke, but they both knew that the other had forgiven them, felt they were sorry, and had accepted each other. After that Mycroft only came once a week, but John supposed that it good for both their sakes, they both understood in ways that no one else could. Mycroft never once tried to take any of Sherlocks things, he knew why John was never going to get rid of them, and accepted it.
John never did get over his grief fully, he never really thought he was, he was always going to love the man. Not in the way everyone thought though, people had treated him like a widower, he did love Sherlock but like a brother (well not Sherlocks kind of brother though) never romantically. Even though he still missed Sherlock, he had stopped crying a while ago, he had got to the point where he could bring up Sherlock with Ms. hudson and not feel as if his chest was being ripped apart.
Then a year, three months, and 17 days after the fall, there was Sherlock in his sitting room, plucking the strings of his violin. The night had ended in a few punches, and some screaming, crying, and just the tiniest bit of laughter, and then eventually John making his way up stairs to his room and falling asleep to a soft melody on the violin.
They were far from better, and John couldn't find it in himself to forgive him just yet, but after a month of both of them walking around each other as if walking barefoot on glass, John had one of those nightmares. The ones that he had had every night for a month after sherlock's death, it had been a while since he had one so vivid. It was Sherlock dying again, and when he woke up there were tears on his face, along with sweat and he had run down stairs to find sherlock standing in the living room looking at him concerned.
He ran to him, and had tackled him to the coach in his arms. He hadn't even thought about what this could look like to other, him pushing Sherlock onto the couch, sitting on his lap and hugging him and crying. Sherlock hadn't said a word and after a few moments had brought his arms around him as well. Johns legs had started to ache, and sherlock seemed to know, along with everything else, and had turned them and laid them both down on the couch so that johns back was to the back of the couch.
John still slightly out of it and desperate had run his hands over every single inch of Sherlock's body, feeling it memorizing it, and Sherlock let him while staring at him with soft eyes. After John was done, which could have been ten minutes or two hours, he finally brought his arms tightly around Sherlock, and buried his head in his chest, and then fell asleep.
He Realized that morning when waking up in Sherlock's arms, to find Sherlock awake and still looking at him that he had been stupid. The one thing he had wish for, had come true, Sherlock was alive, the man he needed in his life was alive, his best friend was here again, and he was going to be happy again. And he was happy, after that they both went back to normal it was like nothing ever happened. Sherlock still sometimes looked hesitant about thing, like what he was allowed to do around John. to say to him, if he was allowed to touch him, and John dispelled all those doubts. In fact they became closer than they ever were.
They both touched a lot more. When Sherlock was taking up the whole couch while he was in his "mind palace", John would lift up his legs, sit down then replace on his lap while he watch T.V., read, ate, or drank his tea. When John was sitting on the couch, sherlock would often lay down and but his feet on John lap, and John didn't once make a protest it was comfortable for them both. He also didn't make a comment when Sherlock started to put his head in his lap when he laid down instead of his feet. Sherlock also expressed a like for hugs, and not just any hugs, Johns hugs, and John was perfectly fine it.