I am now writing rhetorical analysis of the "Molly scenes" and will get to the second season...eventually. Because what better way to analyze the relationships between the characters than through what they say in the script, the absolute canon of the entire fandom?

Episode 1: A Study in Pink

Sherlock: (opening the bag holding the cadaver of interest, sniffing) How fresh?

Meaning, of course, how freshly dead. Why would he ask that? It couldn't have been the first thing he said walking into the morgue. He would have had to ask Molly to wheel the body out.

Molly: Just in. 67, natural causes. Used to work here. I knew him. He was nice.

This trip to the morgue can't have been Sherlock's first as it's only the two of them (well, and the cadaver) in the morgue, and Molly knows what he means by the question. You immediately realize that Molly is just the sweetest thing alive by her last two statements and the intonation of her voice: she really means what she's saying. And, hopefully, you also realize that this job shouldn't suit her. Nice girls don't typically work with dead people. Perhaps this is what intrigues Sherlock about her. There has to be something that does otherwise he wouldn't talk to her as much as he does.

Sherlock: Fine. (he zips the bag closed and looks at Molly) We'll start with the riding crop. (smiles)

I'm not sure what he meant by "we", since Molly obviously isn't helping him with this experiment. Maybe it's a British thing, like "let's". Smile. Yeah, that's what I'd do. That'll definitely make me seem endearing...No, he might be thinking, this is what i do and i enjoy it so get used to it.

(Sherlock violently strikes the corpse with riding crop. Molly flinches from her vantage point outside of the morgue.)

Why is Molly outside of the morgue? Perhaps to gather her composure for the next things she'll say. Maybe so she won't have to witness Sherlock beating up the dead man, whom she knew, though she watches anyway. My money's on the first one.

(Molly re-enters the morgue)

Molly: So. Bad day, was it? (she chuckles nervously)

An attempt at making a joke. Maybe to break the ice for what she's about to ask. Maybe to impress Sherlock with her 'deduction' skills. Probably both.

Sherlock: (writing in a notepad) I need to know what bruises form in the next twenty minutes. A man's alibi depends on it. Text me.

Sherlock obviously knows Molly pretty well if they have each other's contact information. I would say that Molly's wondering what her 67 year old friend has to do with someone's alibi, but I have the feeling she's not really listening, based on her next question.

Molly: Listen, I was wondering. Maybe later, when you're finished…

Her voice starts high here and sort of goes down. Like she's nervous and she knows she's nervous and she doesn't want Sherlock to know she's nervous.

Sherlock: (looks up from his notepad for a second, then does a double take) Are you wearing lipstick? You weren't wearing lipstick before.

He totally interrupts her, which either shows he doesn't care about what she has to say, he has no sense of tact, or he wanted to state his observation. I'd say all of the above, but some of his later statements say otherwise. I love Sherlock's double take! Why would he do that? He wouldn't normally need to look at her twice to observe the lipstick unless he didn't expect it. Which therefore means he didn't expect it. Which means Molly surprised him. Why is Sherlock looking at her lips to begin with? Well, Sherlock does observe everything. He probably noticed something different with Molly, then realized what exactly it was, hence the double take. However, he asks if she's wearing lipstick, which by now he already knows, so he did it to figure out why she's wearing lipstick.

Molly: I, er…I refreshed it a bit.

I'm sure Molly wanted him to notice her lipstick, but it seems like she hadn't expected him to say that he noticed. She's debating for a minute, as anyone trying to impress someone would do, whether his vague statement was a compliment or not.

Sherlock: (slowly turns back to his notebook with a look of ambiguous appraisal) Sorry, you were saying?

She hadn't quite answered his question, which I'm sure annoyed him, but he doesn't pry or deduce much. He doesn't know what she has to say. But he does want to know what she was saying. Why? Perhaps he is trying to recover from his almost-blunder, unsure if he's offended her with the lipstick comment.

Molly: I was wondering if you'd like to have coffee.

She's asking him out. It must have taken her a while to muster up the guts to do that. Which means they've known each other for a while. You don't ask someone out when you've just met them.

Sherlock: Black. Two sugars, please. I'll be upstairs.

Okay. Obviously, this is either Sherlock completely rejecting her or completely misunderstanding her. I'm certain it's the second. If he were rejecting her, he probably would have said so, bluntly at that, or made an excuse.

Molly: Okay.

Poor Molly. : (

(Sherlock is in the lab when John enters. Molly enters at the start of the conversation with coffee)

Sherlock: Ah, Molly. Coffee, thank you. What happened to the lipstick?

He recognizes Molly's entrance first, before the coffee. Coffee is an afterthought, but not something entirely unexpected. He realizes that Molly will do things for him. And he thanks her, ever the soul of tact, or at least keeping his acquaintances close and useful.

Molly: It wasn't working for me.

She had interpreted his observation from before as a sign of distaste.

Sherlock: Really? I thought it was a big improvement. Your mouth's too…small now.

Sherlock attempts to say that his observation was merely an observation, he, contrarily, very much liked Molly's lipstick. But, of course, it comes out sounding more like an insult than before. Then he sort of waves her off, so perhaps this is actually his method for making her leave the room. However, she probably would have left when they started talking again because she's polite and probably wouldn't want to intrude, so this thought becomes more invalid. In that case, she makes him feel uncomfortable. But hasn't Holmes always been a bit awkward around the fairer sex?

Molly: Okay.

Poor Molly. : (

So, yeah! Stream of consciousness over-analyzing! Tell me how I did!