So, we all remember this letter, right?
The letter that John sent to Sherlock
The one that we never got to see or knew what it said.
So I have two theories for this:
The first one (and most viable) is that the letter said something like "I wish you had died for real that day" or "you were better off dead". I got this impression from Sherlock's face when he read it and how it affected him.
The second one (I think a lot of people will disagree with me in this one) is that it was never sent by John and instead was Molly who wrote it. Why, you may ask, because, first, we never saw John writing it nor mention it later on the show. I'm not saying that Molly did it with a bad intention, maybe she thought that doing that she was assuring John's safety, like, his wife just got killed it was just a matter of time until he got himself into a really dangerous situation (which he did in The Final Problem). Now, why she didn't had Sherlock's feelings in mind? Molly knows that Sherlock is not a heartless machine, but she do thinks he overcome this things really easily, so it's natural to think she would think that it's the best for them.
