I asked you for one more miracle.

How is this supposed to be a positive thing, though?  Because Sherlock says, “I heard you,” and then the implicit extension is, “And fucked off and did nothing about it for two years till Mycroft made me come back, because basically I just didn’t want to tell you till whenever I felt like hauling my arse back to London.”

There’s a lot that’s confusing about this episode, but at least it can largely be explained if you accept the concept that John is a supremely fucked-up puppy who prefers Sherlock being abusive to no attention from him at all.

But there’s absolutely no way to make this bit make sense in any way that could be conceived of as uplifting or bonding.