There's a fairy tale I was told when I was little where a man saved a little bird while he was traveling who then turned into a woman and said she would be faithful and true to him always, all he had to do was keep three secrets of hers. She travels with him, generally putting up with him and being the best companion ever as he eventually tells her three secrets to different people (not all at the same time of course) without really thinking about it, because she'd never leave him. She puts up with everything he does after all. But after he tells her third secret he comes home to find that she's gone and he never sees her again.

I couldn't help thinking of that as I've watched John during series 2. (Not that John's a woman :)) So somehow John either tells Sherlock three secrets, which Sherlock eventually reveals; or Sherlock simply betrays John in three other ways and John disappears. Level of fusion/magical realism up to the filler.