I think the writers’ main intra-episode reason for Molly admitting Sherlock used her bedroom as a bolthole was to explain how Sherlock could be dating a sexually forward woman for nearly a month and still not have sex with her (i.e. he hadn’t been sleeping at his flat for weeks).
Before the Fall, I don’t think Sherlolly were close enough for Sherlock to stay at her flat. After the Fall, they were, but while Moriarty’s network still existed, it’d be too risky. I could buy maybe 1 or 2x if he returned to London during the 2 yrs he was dead, *IF* he felt it was safe enough, but Molly didn’t make it seem like a one time deal. And once Sherlock returned, he didn’t have a good excuse or any need (as far as we know) for a bolthole except for Janine staying at his flat.
Additionally, I think Molly specified he used her bedroom, not her spare room bc the writers wanted to add fuel to the Sherlolly shipper fire. There was really no other reason to specify which room, but they did & for that I wish to say thanks.:)
Piecing together bits, my head canon is:
A few days after the wedding, bored Sherlock took Lady Smallwood’s case. He discovered Janine’s connection to CAM & asked her out. After a couple dates, it became clear that he’d have to invite her over to his place to keep up the charade and Sherlock didn’t want to have sex with her (“there are limits”). So I think he visited Molly at her lab, happily discovered Molly was rethinking engagement (after “meat dagger” who wouldn’t?) and was living alone again to to slow things down with Tom. I don’t think Molly had given Tom back his ring and made a total break but Sherlock took this sign of trouble as an invitation to use her flat as a bolthole. I think he was testing the waters on Molly’s feelings for him. Would she let him stay? I think he complained the spare bedroom’s bed was too small for him to be comfortable to see if Molly would give him the big bed (which she graciously did) and then maybe sleep in it with him (which I think she did not). I think this lasted for more than a week wherein Sherlock would take Janine out, they’d head back to his place and before anything got too serious, he’d get an urgent call making him leave for a case at which point he would go over to Molly’s and hang out with her until bedtime. I think Tom found out Sherlock was staying at Molly’s and they fought. Molly, not ready to give up on her engagement with Tom, told Sherlock he couldn’t stay at her place and so an ejected Sherlock came up with his plan to be blackmailed over drug use to solve his night accommodation problem, but it was really an excuse to get high bc he was feeling abandoned and sorry for himself. I think he did this for a couple weeks until John found him.
This would explain how Sherlock knew Molly’s absent ring was from a broken engagement, not an accidental loss or removal for work and why he felt compelled to comment upon it. (i.e. he wanted Molly to know he noticed). I also wondered if Sherlock’s “sorry your engagement’s over” was suppose to have an edge to it bc it sounded a bit snippy to me.
IMO Sherlock was not putting up the polite act about the engagement any more the way he did in TEH and SoT. Yeah, it could be that Sherlock was too high to hide his feelings, but Molly also dropped her shy act. I feel the acting in the scene heavily implies SOMETHING happened btw Sherlock & Molly off screen in that month to change their attitudes towards each other bc Molly at the end of SoT was not set up as someone who would slap Sherlock. It isn’t that she loved him any more or less or that she changed who she was as a character but that Molly’s sense of “standing” in regards to Sherlock must have somehow changed to be a person who could touch him in such a familiar way.
This woman wasn’t comfortable enough with Sherlock to say what was truly on her mind. She whispered it when he was out of hearing range. There is no way, she would have presumed to slap Sherlock bc he was taking drugs. Lectured him? Expressed disappointment & worry? Yes. Of course. But they weren’t close enough for Molly to physically touch Sherlock in such a sharp/hostile and familiar manner.
Fans have been comparing S3 John and S3 Molly and this parallel is to me one of the biggest. I don’t condone it, but both John and Molly assault Sherlock out of frustration with his behavior in s3. This doesn’t indicate diminished affection on either part. It was that they had both reached their tolerance limit for his BS and Sherlock understands that he has betrayed them so he allows both to physically take out their exasperation/frustration on him. It is totally unhealthy, just like Sherlock & it is how the characters get beyond what would be deal breakers in most other relationships.
Sherlock snapping at Mycroft, imo, was an extension of his scene at the lab with Molly. Sherlock blamed his hostile behavior on being high, but he was higher at the lab and he didn’t do anything but passive aggressively bring up her former fiance when Molly slapped him 3x. To me, Sherlock throwing Mycroft ag. the wall was done to show his real mood. He put on a placid facade in the lab, but Molly Hooper slapped him. Molly Hooper saw him high and said he had BETRAYED the love of his friends. And Molly Hooper was single again and that should have made him happy but it was all ruined now and he had only himself to blame for it. So Sherlock took out his shitty morning on his brother bc he had all this anger at himself pented up from the mortifying lab scene and he was itching to let it out.
It kinda stinks that’s where it stops. We have no idea if Molly forgave Sherlock and tried the kind, loving approach after the slaps or if she stayed angry and gave him the cold shoulder. Did Molly urge Sherlock to see a drug counselor or did they awkwardly avoid the topic? We have no idea what Molly’s reaction was to Janine’s stories in the newspapers or to Sherlock being shot. We never see Molly visit him in the hospital, but surely she did. And months pass by the end of the episode and we don’t know what is going on with Molly except she is still working at Barts. Moffat was right. I can’t believe they left it there.