Author's note: I've gone through and corrected all the mistakes and typos I know of. If you find more, send me a PM and I'll go back and fix them!
Sherlock stood in the living room of his flat, fingers steepled, musing. His flat-mate - the one he'd only met a few months ago - was on his mind. John Watson intrigued him, unexpectedly. When he'd met Doctor Watson by chance at St. Bart's Hospital lab, he'd thought little of the encounter. The man had appeared average - former military. Upright, polite, dull. The psychosomatic limp was mildly interesting, but he'd seen similar afflictions before. John had the usual skeptical reaction when Sherlock had begun deducing things about him as if out of thin air. Nothing remarkable. Nothing awful. He'd make a decent flat-mate.
He found the doctor reasonably likeable after spending a short while with him, exploring the new flat. Nowhere near as clever as he'd like, but then no one ever was. John was impressed with Sherlock's talent and he refrained from the usual colorful terms like "freak" or "lunatic".
Still, when Sherlock had noticed the man appeared to be feeling out a relationship over dinner together, he'd uncomfortably balked. Seeing a flat-mate romantically? Did he look that stupid? Sherlock couldn't maintain a friendship, let alone a serious relationship. A boyfriend? Psh. That was never going to happen - he'd already made his peace with this fact years ago. He certainly wasn't going to risk a good rooming arrangement over something as fleeting and dangerous as sentimental attachments. Besides, he barely knew this man, and given the conversation that followed shortly after, it appeared he'd misunderstood the intention anyway. Just conversation after all.
That had been before Scotland Yard invaded the flat on a trumped up 'drug bust' while they were out, and Sherlock had stumbled across a way to track down the serial killer cabbie who'd been forcing passengers to commit suicide. Unable to resist a puzzle, when the murderer had offered to show him how he did it by taking Sherlock as his next victim, the detective had gotten in the car without a word to anyone. In retrospect, he'd forgotten that the mobile tracking that had led him to the killer in the first place was still running, and that Watson was still sitting with it in their flat after he left.
Sherlock was about to swallow one of the murderer's potentially poisoned capsules, unable to resist the challenge, when a bullet broke through the window behind him from somewhere across the courtyard outside and hit the cabbie with deadly accuracy. The murderer had been dead within minutes.
Someone had saved his life, but at the time he hadn't known who. The shooter was gone by the time he reached the window to look out. It wasn't until later, after Scotland Yard had arrived to do something useful for a change, and Sherlock had been using deduction to determine the identity of the shooter for Lestrade, that it hit him. Standing behind the police tape, innocently looking around was John Watson. He fit every criteria. Steady hands- an army doctor, he'd be used to shooting under stress. An excellent marksman, because he'd been trained. He'd had a reason to be there that night, and a reason to keep Sherlock alive. At that moment, he'd seen the doctor in a whole new light.
He closed his eyes, thinking deeply. John was attractive enough, but that wasn't what captivated his attention. The doctor's face and figure were not remarkable, but he was likeable. Sandy blonde hair, cropped close in military style. Dark blue eyes that held a remarkable sincerity, which he had not noticed particularly at first. Short, slightly stocky, muscular. There was something comforting about John. A nurturing presence - probably the reason he'd become a doctor in the first place. Sherlock imagined he made a very good one at that. Something in Sherlock Holmes trusted Watson implicitly, especially after the cabbie serial-killer incident, even as his mind actively rebelled against it.
He was a sociopath. A detective. His brother liked to tell him he had any one of a variety of forms of autism, depending on the day - though Sherlock refused to be subjected to tests. He hated anyone tinkering with his brain. He didn't trust people. He didn't have the time or the ability to be close to anyone… but his mind kept wandering away from case-work to study his flat-mate, no matter how many times he hauled it away.
'A boyfriend'… was he really that obvious? He mused on it a moment. Generally he just told people he was asexual, as it was simpler to explain than 'completely socially-unable homosexual' though that was the more accurate description. He was sure that women didn't register on his radar at all, but the men that did were either stupid, cruel to him, not interested, or some combination. He'd turned to the morphine several years ago as a balm for his emotional wounds, but gave it up to pursue detective work. More constructive. Better for his brain. It kept him busy and he didn't have to think about mundane things like loneliness. He didn't pursue men and they didn't pursue him. Not once they got to know him, anyway.
But John did, after a fashion. Not openly. But he stayed. Not only did he not move out the first time he found eyeballs marinating in the microwave, he seemed almost… fond… of Sherlock. Sherlock was floored to realize, as time went on and they worked together more and more… that John had become protective of him. Anytime something happened, an explosion, assassins… John never failed to ask if he was alright. A small gesture, but it stood in stark contrast to the next closest thing he had, which was Mycroft occasionally making sure he hadn't blown himself up recently. And John wasn't just asking as a courtesy… Sherlock was bad at reading emotions, he knew, but he could compensate for it to a degree. He could, with effort he typically reserved for much more useful things, puzzle out what was meant. John was sincere. Concerned.
Sherlock found himself smiling more and more in the doctor's presence, in spite of himself. He found excuses to keep his new friend nearby. A friend… who would've thought? He didn't let himself consider what else John could be to him. John had made it clear he wasn't gay. Abundantly. Sherlock had studied the denials carefully, and while he was fairly sure there was more to them than their face value, he didn't pry. If he pushed for more, John would leave. And he'd be alone again. Better to have what he could get than reach for more and lose it all.
Things only got more complicated when Moriarty came into the picture.