For ages I’ve been very much in favour of the idea that John has some kind of secret plan that Sherlock doesn’t know about around the time of HLV, like maybe somehow he’s behind the Moriarty broadcast (perhaps with Mycroft’s help) or he really did read the pen drive and never told anyone because he has a plan. I don’t know, something sneaky that proves he’s as good as the rest of them and maybe with a hint of revenge against Sherlock and Mary because they’ve held things from him.
But now actually I think I want John and Sherlock to be working together unbeknownst to everyone else, that together they have a plan that they worked on in equal measure. That those months in which Sherlock was recovering and John was separated from Mary they built a plan to deal with everything and when Sherlock steps off that plane in S4 the game is so very ON.
Just the two of them against the rest of the world.