John was Sherlock's Dom before the fall, so when Sherlock comes back John punishes him but he goes too far and pushes past Sherlock's limits. Sherlock doesn't say his safe word cause he somewhat thinks he deserves it. But sherlock ends up afraid of John because of it. When John realizes this he spends months trying to fix it. Eventually they start down the right path again. But it is only after sherlock tells John about what happened to him while he was gone and they reset boundaries.