Perhaps he should be grateful.
Perhaps he should be grateful that when he came to her, his life in her hands, that she agreed to his plan without so much as a pause or a question. And she had carried out the plan beautifully. Of course she did. She was the only pathologist that he chose to work with. Her eye for detail and her efforts for perfection were far superior than others. Amongst all the chaos, questions, and planning, he had allowed himself to pause, to smile, to confirm that he had made the right choice when had allowed Molly Hooper in his life.
When all the tears, pain and initial grief was over and she came home that day after confirming the death of one Sherlock Holmes, she had gently treated his wounds on her worn-down but still comfortable couch, a reflection of her, really. Perhaps he should be grateful that there were no tears streaming from her eyes. However, he could see the grief and pain that shone in her eyes as clear as day. He knew that she had kept her emotions in check for his sake, because it would make him uncomfortable and even irritable. Perhaps he should be grateful that he didn't have to deal with her emotions but even he couldn't deny the sharp prick of pain in his chest when he heard her muffled crying in the bathroom late that night.
When she allowed him to stay with her indefinitely and had allowed him to take over her apartment, he thought perhaps he should be grateful. He knew that he was alive due to the small, mousy pathologist that was more nervous and awkward than not. He knew that he should be grateful. But he was a high-functioning sociopath. Emotions such as gratefulness didn't come easily to him. While he knew what he should be feeling from John's constant teachings about sentiments, all he could feel was that it was Molly Hooper's responsibility to have done what she had done. But when he woke up every morning to the smell of breakfast and came out to the sight of a coffee with two sugars waiting for him along with the reports of the corpses that had been brought in the past day for his amusement, he couldn't help but smile just a little at having Molly Hooper in his life.
Perhaps he should be grateful that Molly knows him so well and is more than accommodating to his every need, even those that go unmentioned. After a short time together, Molly knows what he needs and when he needs it. Despite his protests that he is completely self-reliant and does not require anyone else, he is still human and there are times, granted they are few and far between, when he craves physical contact. The first time he pursues it, he quietly and gracefully slips in between the sheets next to Molly, more than ready to use the excuse of the couch being far too short for someone his height. He knows that she knows he is there. He can tell by the sudden stiffness in her body when he entered the bed but she does not call him out on it, nor does she turn around even when he falls asleep with one finger wrapped around a curl in her hair. She can read the signs now. She can tell when he is restless and craving human contact but of course, is too damn proud to say anything. At times like that, she will slightly brush past him, shoulder bumping shoulder or she will reach up and touch his hair, with the excuse of checking to see if it needs trimming, or she will sit a little closer to him on the couch while they watch TV, leg touching leg, or she will "fall asleep" on his shoulder. Perhaps he should be grateful that she knows him so well and he isn't sure if he is, but he is sure that it is those physical contacts that keep him sane.
He knew for a certainty that he should be grateful to Molly Hooper when he sees her come home after spending time with John Watson, Mrs. Hudson, or Greg Lestrade. He knew that she had spent time with them the minute he heard her key in the lock. Even the sound of the key turning seemed defeated. She quietly comes in and unlike the other days where she would smile at him and go into her room to change, she would lean her body against the closed door and look down, the grief belonging to those she had been with cloaking her. He could never see her expression during those times with her hair covering her face but he sees the hand that comes up and rubs at her chest as if to ease the pain. He does see the expression, though, when she finally looks up at him and the detective that he is, he can make out the emotions in her eyes. Rather than seeing the pain that he would think would be there, it is the opposite. He can see the relief and joy shining there. Relief and joy at the fact that he was there sitting in her living room couch, going over the notes that she gave him and not buried six feet under like the rest of his friends believe. And he hasn't seen anyone look at him like that since he was little, since when his mother looked at him when she thought him her "normal" boy, happy that he was there and not Mycroft. (A piece of her heart broke when she found out her youngest son was not so different from her eldest.) And he doesn't know if the feeling he has is gratefulness but he feels a warmth blossom from his chest and spread throughout his whole body. Perhaps he should be grateful and maybe he is, but he knows that this warmth was something more and it was due entirely because of one Molly Hooper.