Disclaimer: I don't own BBC Sherlock. I am just a devoted fan.
Molly Hooper knew Sherlock would be returning someday. She believed and would always believe in Sherlock Holmes. Her relationship with her faith was complicated, but she would never shake it, no matter what he asked of her.
Perhaps some would praise her for her selfless devotion and others might condemn her for her excessive accommodation of the consulting detective's demands, but Molly knew that her choice was selfish. It's not even that she expected Sherlock to reward her years of coffee bringing and rule bending with a more personal relationship. Sure, she hoped. Who wouldn't hope when confronted with Sherlock Holmes' eyes and voice and mind? But trying to win his attention and his affections was only a small part of Molly Hooper's motivations.
So many people called him names, put obstacles in his way, and she had long ago vowed to herself that she would not be one of them. No matter how cruel he was, and Molly had called him out on his malice that Christmas, Sherlock made the world a safer, better place. She didn't care that he sought primarily to appease his need for puzzles. After all, working in the morgue had taught the pathologist that life was for the living. The dead could not be hurt by inappropriate humor. That is not to say that she treated or supported treating her patients with anything less than respect, but she understood the thrill of a correct diagnosis that outshone her compassion for the victim.
She understood him, sometimes. Wanted to understand even more. Saw him as the greatest of mysteries. Yes, he flustered her with his self-serving flirting and his harsh comments, and his intimidating perception. But Molly respected him. Her behavior was not simple idolatry, nor was it mere lust for sharp cheekbones and great hair.
He had so few people on whom he could count. John was the last – the one who truly changed him. Although she had thought she didn't count, doubted even now at times that her years of service would matter if she hadn't happened to be convenient, her insecurity only went so far. No, Molly had committed herself to her path. If sometimes, watching Sherlock fuss and complain, she thought of changing her stance, of leaving at the end of her shift instead of staying late, Molly swallowed her frustration with the detective. She chose to help him, to put him first, because she loved him, she trusted him, and she knew no one else who could do what he did.
So Molly Hooper selfishly kept Sherlock's secret and waited for the day he could return. As much as she relished the trust Sherlock had placed in her, she knew that one day she would have to truly earn it – and let Sherlock return to his real life unfettered. She would keep her word to herself. And she, Molly Hooper, would continue to aid Sherlock when she could, not expecting anything, simply because she believed in him.