Holmes relied on the science of deduction in every aspect of his life. It explained how he came to every one of his conclusions: following each thread until their unraveling, leaving no logical option unexplored. With all the evidence presented before him, he pieced together the details into a much larger picture.
Deduction had allowed him to analyze, within seconds, the professional and personal past of Dr. John Watson upon their first meeting. He had observed a soldier and army doctor, both shattered and strengthened by his experience in the war; a man who found himself completely alone, with a broken family and no support. It had made things easier, then, for Holmes to become that support as Watson's flatmate.
Watson's quick loyalty allowed Holmes to immediately rule out temporary flatshare arrangement. The first time Holmes had warned Watson of the danger associated with his cases, Watson had agreed in full knowledge of the extreme risk. Watson had, more than once, fired his army revolver on Holmes' behalf, more often than not saving the detective from a life-threatening situation. Flatmates became friends as a result of Watson's loyalty and trust.
When Holmes fell ill from weeks of overworking himself, or came home bleeding on the carpet from a bullet wound, Watson became caretaker. When Holmes shared his theories and wanted input, Watson became colleague. When Holmes acted morose and moody, choosing silence over conversation, Watson became deduction personified, able to crack through the detective's brooding.
The science of deduction Holmes had perfected into an art. The only problem with deduction was its lacking in answers when emotions were concerned. For a long time, Holmes had tried to turn off his emotional side, to become solely a brain meant for logic. But he was still human, and still had a heart to burn. In the realm of emotions, logical deduction was futile at best.
So he sat turning things over in his head, presented with a full set of evidence. Only this time, his case was himself: his behaviors, his thoughts, and his blasted emotions. Before, he would easily let the details of a case occupy his consciousness, occasionally having them clarified by Watson's presence. Now, he only noticed Watson's absence when he was trying to think. He felt his heart race and his chest swell with pride whenever they sat together in the sitting room, sharing a comfortable silence. He worried about Watson when he was with patients, for no logical reason at all! He ran faster during chases to protect Watson, ensuring the way was clear.
During the nights, all of Holmes' thoughts were at their worst. Wonderful dreams of him and Watson sharing a bed in the throes of passion terrified Holmes to the point of refusing to sleep at all. He stayed awake night after night, trying uselessly to deny the truth. He desperately sought out other explanations, any other train of thought he could entertain other than the obvious. But every time dawn broke over London it also broke unto his consciousness. Holmes was falling steadily in love with his best friend, but love between two men was a crime against the Crown. Sherlock Holmes, consulting detective, was a criminal.