As crazy as it sounds, it could be true.
I recently saw this theory on tumblr not that long ago. At first my reaction was "PPFFFT. REALLY. REALLY?!" But after looking around on Sherlock Wiki there's a trivia at the end of her page with the following:
-Molly has a cat called Toby
-Molly is a nickname for Mary
-A dog called Toby was introduced in The Sign of Four, the same story in which Mary Marston also appears (??)
So yeah, go forth and discuss!
And as always, DFTBA
It's a good theory, but it seems that she doesn't notice John very often during the show. I do like the idea of the two getting closer following the funeral, but I don't think that it will ever get romantic.
Actually, Mark Gatiss and Moffat have both explicitly stated that Molly is the only character not to have a counter in the canon Sherlock Holmes stories. Also, it takes Molly like three episodes to even remember John's name, whereas in the canon, John and Mary have a better connection than just my crushes best friend. You could argue that they will get together in the years of Sherlock's disappearance, but do you really think he could forgive her after she, hypothetically, lied to him about his own best friend's death? Molly is the only one who knows about Sherlock's faked death.
I don't think Molly Hooper is Mary Morstan.
This is the Godtiss machine though, they are the ultimate trolls. Like the rat, bow, wedding clue, which is /probably/ The Adventure of Charles Augustus Milverton.
I didn't know Moffat and Gatiss said that. Hmm.
Though, the idea of Molly and John becoming close is a nice thought (if she had nothing to do with the fake death.) Or maybe, if she did have something to do with it, she could of told John before Sherlock.. AHH! I DON'T KNOW! MOFFAT *shakes fist* all the questions!!
But don't you remember the scene in Reichenbach when Sherlock goes to Molly and says he needs her... the most likely continuance of that is that he needs her... to help him fake his death.
I suggest looking up some of the many Reichenbach survival theories on the internet, and you can see that in most cases Molly plays a crucial part. And I don't think Molly would have spilled Sherlock's secret, even if she was romantically involved with John, she would have known that Sherlock would never forgive her.
In some ways it makes sense...in others it doesn't. It would be really awesome if it were true, but I don't see Moffat being quite that...cute.
More than anything I would love to see something work out for Molly. Sherlock has put her through so much and it would really be cool if anything went right for her. But I don't think John would be the best relationship for her. John is just as obsessed with Sherlock as she is, even though it may not be in the same way, and their relationship would be dependent on their mutual obsession.
It is difficult to tell whether Moffat and Gatiss will even bother bringing Mary in as a character, since so much of the comedy seems to be wrapped up in the ersatz homosexual relationship between John and Sherlock.
... But they have talked about how they will deal with John moving out and not living with Sherlock any more. As he does when he marries. So they probably will.
I would love for Molly to actually be Mary, I just think that all the signs kind of point towards that, or maybe Moffat and Gatiss are just teasing us. But the thing is, Mary dies in the stories, because Doyle didn't think the dynamic of MarriedJohn/Sherlock was as good as BachelorJohn/Sherlock, and so if Molly is actually Mary, that would mean, they might kill Molly, but then again, almost no one actually stays dead in Sherlock...