A/N: Unbetaed, sorry, not currently got a beta for this fandom.
Tom has no idea of the secret she hides. She likes that. He doesn't judge her for her defence of Sherlock either, not like her friends tend to, who think she has wasted years pining for a friend who was a fake. When she accidentally uses present tense to talk about Sherlock she doesn't worry with Tom, she corrects herself and he believes it's a slip of grief. Tom trusts her and eventually she gets over the fact she's already betrayed him, out of necessity, because he's the least of the people affected by the cover-up.
John doesn't try to talk to her anymore, but Mrs. Hudson sometimes calls, concerned and fretting over John's silence. Greg comes by the morgue every now and then, for a case consult usually but sometimes just for a quick commiserating cuppa in the canteen. With those conversations she needs to be on guard but they only happen from time to time and eventually it gets easier to pretend. The lie settles in for long haul. So does Molly with Tom; they have fun and she's found she really needed that, an escape. Everything is getting simpler now.
Then she is staring at Sherlock reflected in her locker mirror. Then he is inviting her to 221B. Then she is on a freaking case. Cases, plural. A whole day alone with him. She doesn't kid herself, even though he says she's not a replacement for John, she blatantly is in part. If there's one thing she doesn't trust Sherlock entirely on, it is to know how he feels. But she knows how she feels as he leans in to kiss her on the cheek.
This time she wants to apologise to him almost, for moving on, just like John has. Forced to leave him at the end of the day, other obligations, not simply work. She'd seen him eye the ring several times that day, more obvious than he might think, so she hadn't been surprised when he'd said the expected social response of congratulations but she had felt her heart skip a beat. She'd never pictured this, she isn't prepared.
She goes home, glad she doesn't have to see Tom on the same night. Every time she sees Sherlock after that she reminds herself she doesn't know how he feels, no matter what she thinks she read from what he did, what he said, how he held himself. Of course she knows exactly how she feels, about Sherlock, about Tom. All those carefully prepared reasons to like Tom, presented logically to Sherlock and it wasn't because Sherlock needed to know, nor that she intended to convince him. She'd wanted to convince herself a bit more, see if he'd agree and reinforce her choice for her.
The sex is still very good and everyone is so happy for her generally. Life is easier this way, but the element of care-free she'd lusted after with Tom has worn off now Sherlock is back and she's left with a complicated set of feelings, a cross hatch of thoughts about her men, only one of whom is actually her man, that intersect dramatically in her mind. Like the dissection of Tom by Sherlock that had never come but she fills in herself in the dark, in the restless minutes before sleep claims her. She'd introduced both elements together but no real reaction was evident. She doesn't know what to make of that. Unwisely, she tries when she sees Sherlock to get a rise out of him, dropping a comment about the one particularly good thing she does have with Tom, seeking proof of what she hopes.
The problem is she's always hoped he might return her affections, so she's not about to give up what she has for a futile fantasy resurrected. Sherlock is back and he is different; doesn't mean he's the kind of different that makes him perfect for her suddenly. Molly still dreams. Her head tells her Tom is a good man as he is, a good choice, reliable, but her heart wants brilliant, jumps at the idea of adventure, that risk, the unknown she got a taste of for a single Saturday.
She brushes it off as cold feet and the grass is always greener syndrome, all the things people warn will happen as your wedding planning progresses and the big day looms. Tom doesn't notice, she's gotten great at hiding things from him with smiles and deflections, suggestions they go to the pub or play a board game. That would never happen with Sherlock. Sherlock would know, Sherlock would say something, call her out on it. Except that would never happen, her with Sherlock, and Sherlock doesn't say anything about her sort-of-lies because he wants her to be happy. You deserve it. He must think she'll be happy with Tom finally, that her second guessing is wrong, not her first acceptance. Whatever it is, she does think she deserves it. She's made her bed and now she lies in it.