When Sherlock fell, he had his brothers' help, and before he completely vanished, made Mycroft promise to protect all those close to the detective. What Sherlock had not expected, or anticipated was that it would ultimately be Mycroft who needed the protecting the most.
Habits and routines were the only things that first held them together. John needed stability post-fall, Greg Lestrade offered that up in the form of taking him out a few nights a week to drink their sorrows away. Mycroft was showed up late in the night and made sure that both made it back home in one piece. He had promised his brother that the two friends he had would survive until he was able to return from the dead.
This was the routine that they developed for that first year of Sherlocks' absence. During that time, John seemed to have improved, catching the eyes of a young beautiful woman near his age, Mary Morstan. As for Greg, he finally left his wife for good it seemed, and fell further as John improved.
During the middle of that second year, and just after Greg's divorce became final, the routine the three had developed had begun to shift. The DI had taken to badgering Mycroft to join him and John, saying that all the bad water was under the bridge between the government servant and former soldier. Eventually the coppers' attempts began to break through and what was thought of as a simple friendship bloomed into a relationship.
John was not surprised by any of this in reality after the first couple times of meeting up with the two. Lestrade had been secretly pining for Mycroft, the reasons at first baffled John, but they did share a common bond. Greg helped Mycroft get Sherlock out of his drug habits at first, and well Mycroft seemed to be a brick wall not wanting to let anyone in. One drunken night had changed that, and the two were now living together by the second anniversary of Sherlock's fall.
The routine of going out to the pubs and bars bi-weekly had not gone away though. This was going to be their downfall, and all would realize how having a routine like this would be a very bad thing for one British official.