John has trust issues. Sherlock's manipulated him many times (Baskerville, Reichenbach, the bomb on the train). Mary lied to John about her past. John's tried to put all of that behind them, but one day Sherlock lies to him one more time about something. It's something not even that bad (comparatively, for Sherlock anyway), but it rattles John just the same. Mary backs Sherlock up on it (again) saying John's overreacting. John just snaps. He leaves. He just has to disappear for a while and decide if he still wants Sherlock and Mary in his life.
Meanwhile Sherlock and Mary are frantic to find him. In the process of trying to track him down they learn more about John's past and exactly why John has trust issues to start with. Maybe one or both of John's parents were abusive. Maybe Clara was John's beloved fiancee when she started having an affair with Harry. Maybe something happened to John in the army. Maybe all three and more. Whatever it is, Sherlock and Mary finally understand how damaged John really is and vow to make amends and truly earn his trust. Now if they can just find him.
A John/Mary or Sherlock/John or Sherlock/John/Mary ending is all fine by me, or even John leaving both of them for good.
TL;DR John disappears after Sherlock lies to him again. In the process of trying to find him, Sherlock and Mary discover why John has trust issues in the first place.
Trust issues and John's past - John finally breaks down and walks away from his life
Meanwhile Sherlock and Mary are frantic to find him. In the process of trying to track him down they learn more about John's past and exactly why John has trust issues to start with. Maybe one or both of John's parents were abusive. Maybe Clara was John's beloved fiancee when she started having an affair with Harry. Maybe something happened to John in the army. Maybe all three and more. Whatever it is, Sherlock and Mary finally understand how damaged John really is and vow to make amends and truly earn his trust. Now if they can just find him.
A John/Mary or Sherlock/John or Sherlock/John/Mary ending is all fine by me, or even John leaving both of them for good.
TL;DR John disappears after Sherlock lies to him again. In the process of trying to find him, Sherlock and Mary discover why John has trust issues in the first place.