Sherlock was by nature rather flexible in his emotions. He had been accused on more than one occasion of possibly being bipolar and thus it was really no surprise that his emotions ran both high and low.
John had never actually expressed such accusations but then again Sherlock had heard him muttering under his breath about the possibility of slipping both antidepressants and lithium into Sherlock's tea. These were possibly just the musings of a very frustrated flatmate but never the less they implied that some of the more pedestrian diagnosis to explain Sherlock's mood swings and odd levels of extreme or no energy had in fact migrated to his long suffering flatmate.
With this in mind it was not entirely surprising that waiting for John to slowly, one could say incrementally, regaining his physical and emotional equilibrium was something akin to torture. Some days would be absolutely fine. John would soldier through, keeping up appearances and Sherlock would be modestly hopeful and not actually all that bored since reminiscing about childhood events, which included a lot of telling nasty stories about Mycroft's shortcomings had become something of a favourite with John.
At other times however John would shut down. He would refuse to talk to anyone, stop eating, not touch his tea and if Sherlock was lucky he would yell at him for telling nasty stories about Mycroft. The yelling and swearing was infinitely preferable to the days when John would just lie there, curled up like a pretzel and act like Sherlock wasn't there. Those days Sherlock thought that they would never make it out of the clinic ever again. He would never admit it to anyone, not even really to himself beyond a factual analytical thought but there were times when Sherlock thought the clinic might turn into John's permanent home, that there would never again be the two of them in Baker Street solving mysteries and giggling at inappropriate things.
After the first month a frustrated doctor manages to convince Sherlock that it is in John's best interest that Sherlock move back to Baker Street. It is not until John himself informs Sherlock that unless Sherlock moves back home so that John can prove to the doctors that he can actually manage on his own for more than half an hour he will not be released that Sherlock relents.
He wants John home, he wants things to be normal again and this suggestion that John might be allowed to leave the clinic should therefore be a relief. Oddly it isn't. Sherlock lies on the sofa in 221B and stares at the ceiling and worries. Sherlock who never used to worry about anything, other than e a stable fixturepossibly how hard it was to get fresh body parts as a private individual, worries enough to keep him up at night. He doesn't trust himself to care for John. Admittedly he doesn't trust the people at the clinic either. Still between them they seemed to have been doing a decent job at keeping John alive, if not always well. How will he possibly manage on his own in the flat with John without driving either of them insane.
He starts on the impossible project of clearing the flat of all objects that John could possibly use to cause himself harm. Somewhere between removing the belts from all of their dressing gowns and starting to question if he could have the windows replaced with bullet proof glass so that John can't break it to cut his writs again he realises that his mission is an impossible one. There is no way that is he going to be able to suicide proof the flat.
In the end Sherlock gives up, he sits in the flat and blankly stares out of the windows. He has been working on removing everything that could be turned into tools of self destruction. He debates whether it is better to keep his Bunsen burner which is capable of setting John on fire but which will also probably be a stable fixture (he has been told that such things are important) to John when he comes home. After all, it has been in their kitchen constantly since they moved in.. most likely removing all of the kitchen knives will have the same effect. How on earth is he supposed to both keep John away from dangerous objects and keep things familiar when half of the things he usually kept in the flat were potentially lethal. It was either a safe flat that was nothing like the normal 221B or a potential health hazard which provided a serious danger to John's health even without him wanting it to but with homely familiarity. There was really no god choice available.
His attempts at John proofing the apartment isn't even Sherlock's greatest trial. He has never been alone in the flat before. He's never had to manage for more than a few days without John as a sounding board. Therefore it is a surprise just how lonely he feels. It's hardly the first time he spends time alone. Before meeting John he had prided himself in his ability to function essentially without any real ties to the people around him. John Donne had claimed that no man was an island. Sherlock had proved him wrong, at least he had thought that he had. And then there had been John and Sherlock's solitary island had suddenly become very much inhabited and suddenly the ecosystem just didn't work without John in it. Damn , Sherlock cursed himself, when had he started talking in stupid metaphors, that was John's area, him and his stupid blog.
It doesn't get better from there on out. He visits John every day and the doctors keep promising that it won't be all that long. Sherlock should have known that he and the doctors would not have the same view of what 'not long' meant. After three weeks of solitary nights in Baker Street John finally informs him that he has been cleared to come home. For all of thirty seconds Sherlock is thrilled, until he finds out that it will only be for one night to start with.
Surely if John is able to be home for one night he should be able to be home for two nights, and if he can be home for two nights surely he can be home for three and really by that logic indefinitely.
It turns into something of an argument when Sherlock presents this argument to the doctors at Mycroft's clinic. After twenty minutes of heated discussion Sherlock surprisingly finds himself relenting. When the doctor sternly explains that being at home will be a stressor, it will take John out of his carefully created comfort zone and doing so for more than short periods of time might throw John back into the depths of depression, Sherlock actually accepts that he will have John home for 24 hours only.