In The Great Game, Sherlock does the fake-cry in order to gain information. A few months after that, in order to solve a case, John tries to be helpful by pretending to be upset and starts crying so to get a reaction from the witness/suspect/etc. He actually thinks he's not doing a convincing job of it (he knows he's not a good actor) but what John doesn't expect is that his (fake)crying seems so genuine that Sherlock and Lestrade (and whoever else present) think John is crying for real.
Cue everyone tries to comfort him and John being confused. Sherlock being protective (because he thinks someone has hurt John) is a bonus.
John can (fake)cry too
In The Great Game, Sherlock does the fake-cry in order to gain information. A few months after that, in order to solve a case, John tries to be helpful by pretending to be upset and starts crying so to get a reaction from the witness/suspect/etc. He actually thinks he's not doing a convincing job of it (he knows he's not a good actor) but what John doesn't expect is that his (fake)crying seems so genuine that Sherlock and Lestrade (and whoever else present) think John is crying for real.
Cue everyone tries to comfort him and John being confused. Sherlock being protective (because he thinks someone has hurt John) is a bonus.