I love Molly too much to let her be unhappy, so this is my take on the Molly/Tom arc of season 3.
Kind of sort of Molly/Tom, unrequited Sherlolly, implications of unrequited Johnlock. Minor spoilers for series 3 (though if you haven't seen that by now I am judging you).
Reviews and concrit always very, very welcome.
Somewhere deep in her subconscious, she'd always known that Tom was just a substitute.
Inside her own mind she'd denied it vehemently, picking out every single way in which Tom was not like Sherlock. He's really close to his family she'd insist to herself, when does Sherlock ever talk about his parents? And can you imagine Sherlock trying to keep a pet?
Looking back, she supposes that this incessant nitpicking and obsessing over their differences should have clued her in. But she hadn't wanted to look, and she knows it. The moment Tom had walked into that pub in the tow of her friends, and she'd felt the first stirrings of attraction, she'd practically leapt on him. Anything to stop this ridiculous school-girl pining.
She'd managed to convince herself, for a while. Sherlock had been off God-knows where, giving her space, giving her time to breathe. Without his presence, the similarities between him and Tom hadn't seemed quite so apparent. So she'd ignored them and she'd talked herself into happiness. And one spring night, when Tom had gone down on one knee and declared his undying devotion (all the things Sherlock would never do...) it had been so easy to say yes.
When she came across a picture of his ex-girlfriend on Facebook a few weeks later, when she saw her slim stature, mousey brown hair and brightly patterned cardigans, she'd ignored it. When she saw the slightly sidelong glances cast on her by Tom's old friends, the double-takes that they probably all thought were subtle, she'd ignored that, too.
Of course it was Sherlock who ruined it all. The worst part was it wasn't even his fault, not even in the classic Sherlock, I-was-just-trying-to-be-honest-but-wound-up-verbally-sucker-punching-you way. One day of following him around crime scenes, one kiss on the cheek and all her old feelings came rushing back to the surface, making her heart constrict painfully in her chest.
She'd come so far, or so she thought. When she got home that night, it was like every detail that Tom and Sherlock shared had been thrown into excruciatingly sharp relief, so palpable just looking at him felt like an act of infidelity. She'd feigned tiredness, crawled into bed, and fallen asleep with tears leaking down her cheeks.
For weeks she'd continued this way, going through the motions of her life and painting a smile on her face each morning, finding more and more ways to stay clear of Tom. She'd spent as much time as possible at work, among the dead. She'd always rather enjoyed the company of the departed – no feelings to hurt, no lives to ruin.
Then one day she comes home to find Tom waiting for her, eyes serious and brooding.
"Mols... we need to talk." he tells her.
"Oh?" she feels panic rising at that all-too familiar opening phrase. Had he cottoned on? She's not sure what she'd do if he walked out now – a horribly selfish thought, but one she simply can't help.
He gestures for her to sit down, and she does, hands clenching in her lap. He sits next to her, and they both stare at the opposite wall. After a few moments of silence, he says "What are we doing, Mols?"
"What do you mean?" she asks, her voice trembling.
He takes a deep breath, "We've been dancing round each other for weeks like we're afraid to touch each other. Every time I approach you these days you jump away like I'll burn you. A few weeks ago you seemed so happy–"
"I was, I mean I am." she insists. It sounds feeble even to her own ears. "I love you, it's just... it..."
He looks at her, eyes sad. "It's Sherlock isn't it?"
She can only stare at the ground, eyes stinging. Then, to her surprise, he reaches across and squeezes her hand. "It's OK."
She stares up at him, and he amends "Well, no it isn't, but I understand. I guess I haven't been very honest with you either." And he tells her about the ex-girlfriend, Katherine Tooley and her smile that lit up entire rooms, and her fascination with the paranormal and the way she always wore her hair in a side braid. He tells her about the summer they shared, and about the football player who had whisked Katherine away and brought Tom's world crashing down around him. And then Molly tells him about Sherlock.
By the time they're both done talking London has rolled into night, and Molly's eyes are streaming and Tom looks as tired as she's ever seen him.
"I'm sorry." she tells him, wondering vaguely which of a multitude of sins she's trying to apologise for. "I... I really want to be over him."
"So do I." he says quietly. "Maybe... let's not kid ourselves, neither of truly want this." he gestures between them, "We've been pretending all this time. But maybe if we stopped trying to fool ourselves, and we agreed to help each other out, we could both get out of these messes we're in."
She looks up at him, and smiles genuinely for the first time in weeks. "That'd be nice." He returns her smile, and pulls her into a hug. Simple, and platonic, and the first time it's ever felt real between them. "It's probably for the best anyway." she tells him, pulling away. "Molly Mallory would never have worked."
He laughs; a genuine, warm sound, and Molly begins to feel the first stirrings of hope.
They spend the following weeks working away at each other. Molly hardly sees Sherlock at all, but they talk about him, and about Katherine. They gently rib each other about how inept they are at handling their respective love lives, until Molly finds she's completely comfortable talking about it. Until she can utter Sherlock's name without her heart beating out a staccato in her chest.
It's an odd thing, for your fiancé to suddenly become just your friend, but it feels so right, so natural. With Tom at her side, she approaches Sherlock and casually asks after him and John and Mary. She has Tom's back when he goes back to the London Eye where he and Katherine first met. She cries on his shoulder and he sleeps on her sofa when his flat becomes too big and too empty.
One day, several months down the line, Sherlock crashes in on her at work and starts talking about about John's stag night. In a fit of sudden tact he remarks that she looks well, and for a fraction of a second she can only gape at him. Because at that moment it finally hits her: he's right. She's fine, she's absolutely bloody fantastic, actually. She's looking up at Sherlock Holmes and she feels fondness, she feels affection... and that is all she feels. She can't stop the note of elation creeping into her voice, though Sherlock doesn't notice. She ribs him about her and Tom, giggles inwardly at his deer-in-headlights reaction, and lets all thoughts of a future with Sherlock fly away.
She and Tom agree to go to John's wedding as a couple. Nobody knows yet about their shift in status, and it would be mean to cause unnecessary drama to distract from the happy couple. She kept important truths from John for over two years, surely that's more than enough.
So they go to the wedding, make a play of looking in love, Tom makes a fool of himself during Sherlock's best man speech and Molly stabs him with a fork (feelings or no feelings, you do not talk while Sherlock is on a roll). And Molly surprises herself yet again during the reception, when she sees the look in Sherlock's eyes while playing John and Mary's waltz, and finds the only bad feeling to be empathy and concern for a friend. She wonders how long it'll take to get used to this.
One week later she drops round Tom's flat and they open a bottle of wine together.
"So." she asks him, "Ready to break the news?"
Tom groans, "This is going to be hell. My sisters haven't stopped looking at wedding magazines since I announced the engagement and my mum keeps ringing me to recommend venues."
Molly makes a sympathetic noise. "I've got it easy, my mum was never much for wedding planning. She and dad got married in a registrar's office then went down the pub. Admittedly, they didn't have a lot of money back then."
"Fancy swapping families?" Tom asks, draining his glass.
"You wish." Molly chuckles. Then she stares down into the dark red liquid and turns serious, "Tom... I can't thank you enough for these past few months. You've helped me so much. If not for you I'd probably still be crying in the morgue and doodling 'Mrs. Molly Holmes' all over the lab reports."
Tom quirks an eyebrow, "Did you really do that?"
"Of course not." she replies, "But I was tempted a few times."
"Well, likewise." he tells her, "I owe you the world, Molly Hooper."
She smiles, "I might hold you to that one day. When are you going to see your family?"
"Leaving tomorrow." he says, "Spending the weekend down there with them."
"Well, best of luck. Meet loads of pretty girls."
He chuckles, "I'll do my best. And you, give Sherlock hell."
She smiles, then pulls herself from the kitchen table and announces that she should be going. One hug and several promises to call each other later, she's out the door.
Back at her flat she flicks the radio on and stares into space for a long time, thinking about the past few years, about how much her life has changed, about all the things she's done and all the things she wishes she'd done and all the things she still wants to do. She thinks about Sherlock and all the time she's wasted. And then she laughs, and laughs, and doesn't stop for a very long time.