Well, I haven't written fanfiction for a while and never Sherlock fanfiction - however, I couldn't resist jumping on the Sherlolly bandwagon.
I already have a few chapters of this written, we'll see how it goes. Comments are greatly appreciated :)

This is set in an AU, after the pool-scene at the end of S1 which assumes there is no Irene involvement and that Moriarty escapes. However, what has intrigued me is that no mention is giving to Molly/Moriarty again, so I'm looking at this in a dark way that'll make later chapters M. This may involve references to non-con and strong violence. The main focus of this story however, is the Sherlock/Molly hurt/comfort aspect and emotional!Sherlock.

Hope you enjoy!

Chapter One

Sherlock had realised something wasn't sitting quite right with him the day he decided to walk by the river and have a coffee. Usually he didn't buy coffee. It was so difficult to rely on people to make it the right way. The idiocy of the average person overwhelmed him sometimes, especially when they could mess up something as simple as black, two sugars.

However, that morning was an exceptional case. He had had a particularly fierce argument with John regarding the bloodied state of the kitchen table, which had resulted in Dr Watson picking up Sherlock's medical microscope and dropping it unceremoniously into the bin. Sherlock's response had been to take the eyes out of the microwave (experiment be damned) and drop them into John's tea on his way out the door. The angry screams of disgust that followed him down the stairs and into the fresh air had been immensely satisfying. Unfortunately, he had the foresight to realise that he could not expect a warm welcome in 221b for some considerable amount of time.

Without a case to solve he found himself wandering alongside the Thames. Holding the styrofoam cup between his gloved hands he stopped for a moment, leaning his weight against the railings and gazing down into the dirty depths of the water. He hoped the turning of the tide would bring a few interesting bodies up to the surface. That would surely stave off the monotony for a short while. Smirking to himself he raised the cup to his lips and took an experimental sip.

The smirk changed instantly into a disgusted grimace.

"For God's sake-" he muttered angrily, hurling the coffee violently into the river and severely startling an American tourist who was snapping a shot of the Houses of Parliament.

Drawing the lapels of his woolen coat about him in what he hoped was a mysterious and menacing attitude, he scowled at the onlookers and prowled away. He was not in the mood for stares. It had been a whole week since his last case, John had kicked him out of the flat before he could finish his morning tea and now he had spent his last coins on a coffee that tasted like it wasn't even worth a penny. Life was not treating Sherlock Holmes in the manner to which he had become accustomed. It seemed nothing would be easy today.

He tread the London streets, bristling with annoyance whenever anyone so much as brushed by him. The proverbial rain cloud grew steadily stormier over his head of dark curls, and he thrust his hands into his pockets and hunched his shoulders, looking for all the world like a roosting vulture. It wasn't just the bad coffee getting him down, it was the whole criminal underworld. It had been so silent since Moriarty had sunk back beneath the radar, slipping clandestinely from the poolside amid the flurry of flickering red lights. Sherlock wished he had pulled the trigger and blown both himself and the consulting criminal to kingdom come. That at the very least would have been an interesting conclusion. But then John would have gone with them, and in the end that just wasn't on the cards for Sherlock Holmes.

It was very nettling to admit, even to himself, but he cared enough about John Watson not to want him to be blasted to bits by exploding semtex. Friends didn't do that to other friends, at least that was his general understanding if popular culture was anything to go by. This was all still terribly new ground beneath his feet, requiring a great deal more research.

The fact that Jim Moriarty had managed to escape unscathed was a high price to pay for the consulting detective. It was almost like admitting defeat, and Sherlock never gave up.

With this thought in mind he decided to make his way to St Barts, his home away from home. Perhaps there was a mysterious cadaver laid out on the trolley, just waiting to spill the secrets of his arch nemesis. Even if there wasn't, he told himself ruefully, he was sure he could find a quiet nook in the lab in which to hide away and mix chemicals and curse John.

He calculated it would take maybe 5 or 6 hours for the doctor to cool down from the incident with the eyes. He was a predictably forgiving soul. However, if Sherlock factored in the severed foot that John would surely find in the freezer that afternoon it might even take as long as 12. He sighed. He would never understand why John continued to be surprised by his experiments, they were obviously never going to stop being a part of 221b, not as long as Sherlock continued to live there. If he got himself killed or kidnapped in the near future then John could go back to an ordinary fridge and an ordinary life, but not before.

Twenty minutes later he strode into the lab with his usual dramatic, sweeping attitude of certainty, hands in his pockets and chin raised imperiously above the collar of his coat. He expected Molly Hooper (his favourite and most pliable pathologist) to stop what she was doing and pay immediate attention to him. That is what she always did. That is what she had always done.

He did not expect to find Molly Hooper sat very still at one of the lab benches, her hands folded loosely in front of her, her gaze fixed unseeingly upon the opposite wall. She didn't even flinch when the heavy fire door slammed shut behind Sherlock's entrance, acting as though she hadn't even heard the noise at all. There was something off-putting about the way she was holding herself, her back straight and rigid, her ankles precisely crossed beneath the high stool.

Sherlock examined her for a brief moment, his attentive eyes flicking over the details of her person. The same outfit she had been wearing for the past 3 days, a small white stain on the front pocket- maybe mayonnaise, from the sandwich she ate for lunch yesterday- high ponytail, the hair pulled uncomfortably tight, dragging at the skin of her forehead and the nape of her neck, a slight greasiness to her T zone- not showered properly over the course of the last week- very dark circles beneath her eyes, slightly sunken cheeks, redness about her nostrils- crying, possibly a cold, little sleep- and she hadn't noticed him, so, dangerously preoccupied.

"Molly?" he ventured, loudly.

"Oh!"

She snapped out of whatever reverie she'd been caught up in, dragging her large, brown eyes away from the mass of equipment ranged across the shelves in front of her. Her fingers knitted together atop the files she'd obviously forgotten she'd been perusing, and she forced a tight-lipped smile that made Sherlock feel uneasy in the pit of his stomach.

It was the sort of expression he just didn't associate with Molly Hooper.

"Anything the matter?" he enquired in as candid a voice as he could manage. He didn't usually ask things like that. Not with Molly.

She stared at him for a full minute in silence, her lips parted as though she wanted to say something but couldn't quite find the words, then she shook her head and glared at the table top. He could see the gulp as it both rose and was suppressed in her throat. He narrowed his eyes minutely, rocking back a little on his heels as he waited, feeling cripplingly awkward. She didn't speak.

"John kicked me out of the flat again," he offered lightly, trying to distract her from whatever she was so intent upon brooding over. "I was experimenting on toads, trying to ascertain at what voltage their skin would sizzle. A lot of moisture when it comes to amphibians, you see. Great conductivity. I went a bit far and one of them burst."

"Oh."

"He didn't like the mess."

"No, I guess he wouldn't..."

"The toad wasn't alive or anything-"

"Sherlock."

Molly's tone brought the detective up short and he stopped talking abruptly, finding that she was staring at him. Her expression was oddly unreadable, a new thing for Sherlock. Usually a woman had to be buck-naked before he lost his powers of observation. He blinked, frowned, and waited.

"What is it, Molly?" he pressed, becoming impatient. "You're being... not good."

"And why is that, Sherlock?" Molly said, throwing up her hands, obviously trying to keep her voice under control but failing. There was a prickly undercurrent of emotion that made Sherlock's eyebrows rise in apprehension. He fully anticipated one of those awkwardly sentimental soul-searching moments that people like Molly liked to have. He couldn't decide whether he found it endearing or annoying.

Wait. What?

"You really have no idea?" Molly sighed resignedly.

"No." He drew out the word and canted his head to the side, "Should I?"

There was a very pregnant pause in which Molly just gazed at him, then she shook her head for a second time and snorted bitterly. Sherlock's frown intensified. He moved further into the lab, approaching her bench in a few, quick paces. He hovered across from her, floundering to discover some floating social cue. Molly was watching him, still with that odd look of barely contained disappointment.

"Have you been sleeping properly this week?" he asked flatly.

"No," she replied softly.

He examined her critically from head to toe. There were healing bruise marks around her neck and the barest trace of a cut above her left eyebrow. His chest constricted, but he refused to comment. It wouldn't do to touch on that subject. Over 7 days had passed, certainly, but surely she wouldn't want to talk about it. Must be something else.

"Are you eating?"

"Yes."

"Have you taken any time off since-?"

"No."

Sherlock groused at being interrupted, but let it slide for once. This situation was becoming too stifling, he wanted to leave, but he wasn't sure if he should. Molly was being decidedly un-Mollyish. Surely, that required some attention. Then again, should he be the one to give it? She seemed angry with him. She probably wouldn't want him to talk to her if she was angry with him.

"Do you mind if I use some of the equipment for a few hours? There's an analysis I'm working on... About the toads, you know..." He mumbled the last part and shuffled his feet in uncharacteristic meekness.

She continued to stare at him fixedly, daringly. Sherlock coughed, uncomfortable under her expectant scrutiny. He drew himself up a little taller, trying to regain control of whatever seemed to be happening between them.

"Your perfume's nice today," he sniffed lightly and appreciatively, his face breaking into a charming smile he hoped would relieve some of the tension. "Flowery. Suits you."

Molly's cheeks pinked, but it wasn't the usual embarrassed, happy-to-be-noticed sort of pink which he was accustomed to. It was flustered, but not pleasantly so. If Sherlock was honest with himself it was a completely unfamiliar flush of colour with a wholly hidden implication. She edged back in her stool, as though trying to scoot out of his range of vision, before slipping off it completely and hurrying towards the door to the corridor.

"I'll make you a coffee," she muttered as she scurried by him. She kept her head bent and her white lab coat pulled closely about her, and with a swish of her pony tail she was gone.

Sherlock was left standing in the deserted lab, filled with a discontentment that made him feel very on edge. He realised that he had misunderstood or misinterpreted something vitally important to Molly, some incredibly simple and obvious fact. He had probably hurt her feelings in some way. But he was always doing that, without even noticing most of the time, and she'd never reacted like that before. She got that he wasn't the sort of person to pick up on civil formalities, that was why he liked her.

This was something that required further study.

Molly didn't come back for a very long time, much longer than it should have taken her to brew a single cup of coffee. When she returned she didn't look him in the eye or speak to him directly, just set the drink down at his elbow and slunk away to her work station to continue sorting through the mountain of paperwork she'd been neglecting before he came in. In her absence Sherlock had taken it upon himself to start analyzing some samples and was completely absorbed. He barely acknowledged her presence until he reached out blindly for the coffee he assumed would be there and raised the mug to his lips.

He sipped, paused, then he glanced over at Molly, suddenly riveted.

"This is good," he said, gesturing to the coffee before taking another, much deeper draft. It warmed him, both bitter and sweet and exactly how he liked it. "This is really good, thank you."

Molly looked up from her work in surprise. He didn't compliment her, not ever. Was he trying to make amends? Had he realised?

"That's okay," she shrugged, awkward and blushing in that indefinable way again.

"No really," Sherlock smiled, the corner of his lip turning up in that half-smirk he reserved only for those people that truly impressed him, whom were seldom. "In the whole of London, only you and John know how to make a perfect cup."

As soon as the words were out of his mouth he felt wrong about putting John and Molly together in the same sentence, with that same reverent tone. Molly was eyeing him as though she were thinking the same thing. She opened her mouth to speak, and Sherlock became unsettling fixated on her lips. Her mouth was small, but pert and pretty. Why had he never noticed that until now?

He turned back to the microscope, and flatly ignored her for the rest of the afternoon.

He was right in thinking John wouldn't be pleased to see him upon his return to 221b Baker Street. Though he had only stayed away for 4 hours, he couldn't stop himself from climbing the stairs to their shared flat and bursting into the living room as if nothing had happened. The morgue had become far too oppressive an atmosphere, what with the way in which Molly had been acting towards him. Gone had been the pleasant buzzing of hard brain work, replaced with the niggling feeling that she expected him to say something. It had been hard to concentrate, and that was the most irritating thing of all for Sherlock Holmes. Distractions were not conducive to good experiments, and as much as he hated to admit it Molly Hooper was one big distraction.

John was sitting in his armchair, paper raised ostentatiously before his face in obvious dismissal. Sherlock hovered in the doorway to the kitchen, having divested himself of scarf and coat. He disliked feeling awkward in his own home, least of all when the remedy was apologising for something he felt had been both a justified and hilarious retaliation. He put his hands in the pockets of his trousers and stared pointedly at the back of John's head. He could tell the doctor wasn't really reading the paper. No one could be that interested in an article about changing bus routes.

"Shall I put the kettle on?" Sherlock offered tentatively.

John turned the page of the newspaper and grunted in the affirmative.

In no time at all, Sherlock returned with a tea tray upon which he had meticulously arranged a steaming tea pot, two cups and saucers, a strainer, a jug of milk, a bowl of sugar and a plate of bourbons (John's favourite). He placed the lot on the coffee table and took his seat across from John, leaning forwards with his elbows resting on his knees, steepling his fingers beneath his chin.

"Well," John said, lowering his paper and taking in the sight before him with raised eyebrows. Sherlock had used the best china, he noted with surprise. "You must be sorry."

"Not sorry exactly," Sherlock muttered, his forehead creased in thought. "Let's call it repentant, and leave it at that."

"Right," John sighed, reaching out to pick up the tea pot.

"Let it brew John," Sherlock snapped, gesturing for the man to sit back.

John, sensing something wasn't quite right, did as he was told. Though still bristling from the incident with the eyeballs, he wasn't a heartless bastard. Something was bothering Sherlock, and that in itself was cause for considerable alarm.

The detective continued to glare into the middle distance, hardly seeming to breathe. John waited, rustling his newspaper in anticipation.

"If I were to ask you for advice, would you please try to treat it with as good a grace as possible?" Sherlock said at long last, his words protracted.

John blinked.

"Advice?"

"Yes, John," Sherlock huffed impatiently, trying not to roll his eyes. "That's what I said."

"Advice from me?" John repeated blankly.

"Please don't make me say it again."

"Right. Yeah. Sorry-" John restrained a smirk with difficulty. "What do you need to know?"

Sherlock lowered his hands to his lap and relaxed back into the cushions of the armchair. He picked up his violin from where it was resting by the fireplace and began to run his fingers along the pegs, plucking the strings deftly but quietly. There was a very pale, very light flush rising in his cheeks and John stared, mouth a little agape. It was like walking in on the detective when he was naked, far too vulnerable a sight.

"When I went to St Barts today," Sherlock began in a carefully flat, unfeeling tone. "I got the distinct impression that Molly was upset with me."

"She's always upset with you," John ventured uncertainly, "You act like a total dick."

Sherlock shook his head the merest fraction.

"Not like that," he said. "It wasn't like the times before. When she's upset with me it's because I've said something wrong or inappropriately blunt, but today I most certainly didn't. I hardly spoke and she just stood there, looking at me as if I'd done something terrible. She's never done that before."

"Why do you care what she thinks of you? You never care what people think." John asked curiously, already hazarding a shrewd guess. No matter how brilliant Sherlock was, he was remarkably dim about some of the most basic of things.

"I like her, she's a colleague. I don't think it's practical for her to be mad at me." Sherlock waved the question away as though it wasn't important and John shook his head and suppressed an immature snort.

"What did you say?"

"Anything the matter?" Sherlock deadpanned, looking up at John with a bewildered shrug. A very unnatural gesture for him. "Surely, that's a nice thing to say?"

John hummed, but inside he was rolling his eyes. Really, Sherlock?

"Well?" Sherlock prompted, his blue eyes searching John's critically. "What did I do?"

John sunk further down in the chair and fixed Sherlock with a level gaze.

"Tell me," he began. "When was the last time you saw Molly?"

"A little over a week ago," Sherlock replied at once, displaying a reassuringly normal grasp on his own internal calendar.

"And what has happened between then and now which might make Molly act differently?"

John felt like he was guiding a small toddler through its baby steps when Sherlock displayed nothing but a blank expression completely devoid of understanding. His lack of emotional depth was truly maddening sometimes.

"Our consulting criminal." John prompted testily, deciding to attack the tea tray in order to avoid punching Sherlock in the face. "Do you want a biscuit?"

Sherlock nodded dumbly and accepted the cup of tea John poured for him, his mind plunged into a sudden flurry of new questions centered around one maddening individual. Moriarty, and more importantly, what he had done to Molly.

What indeed? Update soon kids.x