Disclaimer - I do not own Sherlock, any of the characters or anything like that. At all. Ever. Pinky swear.
Author's note - I don't know if I like how this turned out, so I'm gonna put it up initially then see what happens from there. I hope you like it!
Mind over Matter
What is the mind? Doesn't matter. What is matter? Never mind.
"Put the kettle on, will you John?" Sherlock called as he strode across their living room, depositing his coat over the arm of his lounger and slowly sank into it, lying down and folding his hands on his chest, his scarf falling to the floor. He closed his eyes, the exhaustion showing from the late-night chase they'd just been on.
Watson limped into the flat a few steps behind, sighed at the sight of his flatmate already sprawled out, his mind no doubt whizzing at a million miles a second, plotting the next step of both the killer and the police force. John shuffled into the kitchen, yawning deeply, and flicked on the kettle. He stretched, yawned again and flopped down into the chair that he had sat in the very first night he set foot in the flat – which was now thought of as "his chair". He sighed again and his heavy eyes began to close. Soon he was fast asleep.
Sherlock was awakened by the sharp 'ding' of the kettle as it finished boiling. He looked over at Watson and smiled – a shy and gentle smile. He began to think – rapidly, as he always does – about what it meant to have John in his life.
On the one hand, he had half convinced himself that allowing John to move in was for business and financial purposes only – he worked better with a partner and a flat share was easier on the wallet than living alone in one of the most expensive areas of London. He thought better when he thought aloud, having another person to bounce ideas off made him seem less crazy – well, less outwardly crazy anyway.
Besides, having John live here was clearly doing him good as well – every time they got a case, John's limp seemed less pronounced and his hand stopped trembling. It was only a matter of time before the symptoms of Post Traumatic Stress eased off and stopped completely. And John being a doctor was always good for casework, especially a military doctor – it had already proven once that it can be a handy thing having a crack shot around in times of need. John said himself that he enjoys a more exciting life too, so clearly that's the reason he's around.
But Sherlock couldn't silence the other half of his brain. He looked at Watson, his chest rising and falling in the steady pattern associated with very deep sleep. All the trouble and pain that John suffered when he was awake had completely left him in his sleep. He looked almost... normal. The detective felt his heart skip a beat and he bit his lip, a confused look spreading across his face. For all the times he'd solved murder cases, for all the times he'd caught serial criminals and had them locked up, for all the times he'd stopped innocent people from going to prison for crimes they didn't commit, his genius' brain still couldn't figure out emotions.
Every time he looked at Watson, he felt a surge of emotion and his thoughts spun more than usual. As much as he loved being a high-functioning sociopath, sometimes he wished he could just...stop. Just for one night. Just so he didn't have the confusion over this...friendship? Relationship? Sherlock didn't know for sure any more. Sometimes, when he looked at Watson looking confused after hearing one of the reams of thought that came from Sherlock's mouth, Holmes wanted nothing more than to take John's face in his hands, stroke his cheek and kiss him – but he squashed that feeling with insufferable logic every time it arose.
One thing Holmes knew for certain is that Watson didn't know how much he meant to Sherlock. On the surface, they were flatmates, but Sherlock had never had someone be so tolerating of his depressions and his euphoric moments, of his violin-playing at all hours of the night, of them running everywhere (even though John has a psycho-somatic limp), of his raving tangents that led seemingly nowhere, of his cutting wit and dry, dark humour.
Sherlock sat for a few minutes longer, pondering further and at last, he came to a conclusion, simple but true. He was falling for John, and there was nothing he could do to stop it. Sherlock watched Watson sleep for a few moments longer, got up, put a blanket over John to keep him warm then grabbed his violin and began to play a slow, sweet melody.