Oh, man, I love the acting, writing and direction in that scene.

I think Molly is trying to say that Sherlock is putting on a "brave" face in front of John during this whole Moriarty situation to try to protect him, but Sherlock isn't bothering to maintain that facade when John isn't looking.

Some of the lead-up to that line involves Sherlock pensively mumbling, "IOU."  Molly asks him what he means right as John passes in front of them to move to the other work station, and Sherlock just stills and watches John very carefully, not responding until John is safely out of earshot.  Molly appears to notice this, which prompts the comparison to her father.  Her father was "not okay":  he was experiencing deep sadness at his impending death but didn't want to burden his family with his personal grief (a natural reaction not to want to burden loved ones).  Molly sees how Sherlock is acting one way in front of John and another way when John is absent and deduces that Sherlock is likewise "not okay."

I find it to be an interesting contrast with the 221B scene just prior to the pool scene in The Great Game.  There (at least how I interpret the scene), Sherlock waited until John left the flat so that he could (somewhat gleefully) engage in his game with Moriarty because he didn't want John in the way or judging him again about seeking out the thrills.  Now, it's not that he wants John out of the way to engage in games of which John would not approve.  He just really, really wants to protect his one friend from everything - not just the physical danger of another bomb-vest-type situation (after all, John is Sherlock's "pressure point" as Moriarty referred to it), but also the emotional burden of facing the truth that this may be a battle that Sherlock cannot win.

kazza474 wrote:

When Molly says she's getting something to eat & does he want anything, I think he was going ask her then about her helping him with the plan but decided to wait to see how things panned out

I think he was genuinely surprised by her "I don't count" comment and he was going to ask for something as a weird way of letting her know that she does and he does appreciate her.

I think Sherlock DOES look sad.
I mean not sad sad as normal people do... but in his Sherlock way. Molly knows him well enough and is quite observant, so she notices that.
He looks sad when John can't see him because he knows what is about to happen. He knows that he probably needs to fake his death eventually - he isn't sad because he thinks he might actually die, no, because he already planned everything out.
But he knows that faking his death means that he will have to make believe he's dead to John (Mrs. Hudson, Lestrade...) and he knows how much this will hurt him (them). And that makes him sad - the pain this is going to cause to his only friends.

kazza474 wrote:

Hmm, perhaps. That's if he usually cares about people's low self esteem.

I think he's beginning to care.  To me, I thought he almost looked hurt when Molly said "I don't count".   And I, too, felt he was going to take her up on the chips offer in an effort to be more "friendly". 

But I'm fully aware my intpretations are based on what I WANT them to mean.  I want everybody in Sherlock's world to be happy. 

I love that there can be so many interpretations of this scene based on our own viewpoints of the show. Here's mine.......Molly surprises us (and Sherlock) by her astute and accurate observation of sadness when John is not looking.  He has been keeping a neutral demeanor for John because he knows what the end result is likely to be in a final showdown with Moriarty; but he hasn't realized how closely he is being watched over by, what is to his mind, a rather flighty young lab woman. Nor has he realized the depth of her knowledge of him. I love how he slowly comes up from behind the microscope and really, really sees at her for the first time. "You see me."  "I don't count."  That line breaks my heart because on one level I interpret it to mean "I don't count because you are blind to me.  You don't bother hiding from me because you don't even see I'm here."  But on an even deeper level I take it to mean that she now realizes who does count in Sherlock's life....and it's not someone she could ever compete with.  The unspoken line is "I don't count, but he does."  BTW, when I first watched the show I wondered why she said the line because we really don't see Sherlock looking sad in the lab scene.  But when ran it again I saw a moment I had missed earlier.  We see Sherlock look at John in the mirror when they are getting ready to leave for the Moriarty trial and we see a quiet, sad expression on his face.  He "knows" even then.  This moment is "reflected" back later by Molly's comment.

Yes, wow. I believe that is Sherlock looking into the mirror with his serious face on; not really a sad face.

I think we need to defer to the intuition of the characters. Sherlock may not look sad in a traditional sense because admittedly he does not display emotion the way the rest of us might. He only wears certain emotions, for example, disdain, exhilaration and boastful pride and the like on his sleeve. But Molly is around Sherlock every day and surely through trial and error and by accumulation of bumps and bruises in jousting with him, she has a sense of him. I would strongly bet she has it right.

Sherlock Holmes wrote:

Does Sherlock really look sad when he thinks John can't see him? And if so...why???

If you were scared senseless of an enemy that wanted nothing more than to stick you in an oven and burn you to a crisp like an overdone gingerbread man, and if you were afraid that your partner was going to be extremely badly hurt over the whole thing that was very apt to about to happen to you, wouldn't you look "sad" when you thought he wasn't looking? This speaks to Sherlock's basic humanity, the high-functioning part of his psychological make up. It makes me want to hug him.

MaggieM wrote:

Actually, I found that moment VERY suspicious. I didn't see anything but standard poker face from Sherlock at that moment, so Molly saying that was a BIG mistake. Totally out of character for her, especially given Sherlock's behaviour towards her up til that point (with one exception). And his speech to her at the end unusually emotional and gentle ... . I don't think Molly helped him at all. Something else happened beyond what we saw. I wrote more on this in the molly hooper post.

^^ I agree. 

Molly Hooper knows the truth!!

^ Same. I guess Molly just may be REALLY good at reading REALLY subtle facial expressions. (assuming that's what the scene was truly about)