It took time, far too much time in John's opinion, to get over losing Sherlock. It took almost a year for him to stop expecting his flat mate to be there when he got home and even longer for him to realize that his friend was not just going to come sweeping into the apartment, calling him an idiot for ever thinking that he was really dead. He probably should have moved out of 221B or at least boxed Sherlock's things up. Leaving everything where it was- where it belonged- was not healthy. Or so people told him. John seemed to have a habit of doing things that weren't healthy for him- running after a mad man chasing criminals among them.
So it was in this way that John Watson lived for two years, stubbornly refusing to accept Sherlock Holmes' death. Eventually, however, his grief ran out and John began to move on. He started dating a particularly lovely woman named Mary, began to slowly clean up old experiments, and even stopped visiting Sherlock's grave regularly. To most though, this was not progress enough. He still did not move out of 221B or allow anyone else to move in, nor did he remove anything other than the experiments. Some part of him still believed that Sherlock would come home.
And that part jumped for joy on the third anniversary of Sherlock's death. John was about to leave to visit the grave. He had told Mary that he didn't want any company but she turned up anyway; content to simply wait in the cab if that's what he wanted her to do. She was outside trying to flag down said cab, not noticing the tall dark-haired man with the collar of his long coat turned up brush past her and up the stairs. John certainly noticed him, though, when he opened the door.
"John, what on earth did you do with my toenail experiment?"