When John returned, it did not take long before the two were back to business as usual. Sherlock had been eager to take cases while John was away, so he jumped at the opportunity. And although Sherlock could keep John constantly working through a case, there was still a breaking point when John would let him know that he "needed to sleep like a normal human being," and would flee downstairs to 221C and his wife.
Molly would usually see Sherlock a lot less during cases- unless there was a reason for him to come into the morgue. Molly didn't mind the lack of time spent together while he was on a case though, because his work made him happy, kept things interesting for him; she kept herself busy during the day, spending time both at work and with Mary. Though she loved that he would always send her a few texts during the day- so that Molly would know that he was okay, and it soothed her.
And every once in a while (during a case), she would wake up in the morning and find Sherlock awake next to her (they slept in the same flat whenever he was not on a case though). His mind would still be completely focused on the case, and of course he didn't sleep, but for some reason when he was with her, listening to her quiet, rhythmic breathing, it would allow him to think more clearly.
They had finished up a case, and Sherlock was pacing back and forth along the sitting room of 221B, talking to John.
"Sherlock, what is the bloody matter? You've been pacing since we got back here."
"I don't understand why Molly doesn't live here."
"Neither do I," he said, and then looked at him more curiously, "why doesn't she, Sherlock?"
"Do you think if I knew the answer to that that I would be asking you, John?"
He rolled his eyes and sighed. "Well, have you tried asking her?"
"Yes," Sherlock stated.
"Wait, really? You asked?"
"I've just said that, yes?"
"Well, yeah, but… this is one of those things, Sherlock, that you aren't brilliant with… I didn't think you'd know how to properly ask."
"Clearly not," he said, continuing to pace, "or she just doesn't want to. I gave her my reasoning, and explained to her why it was logical. It would be beneficial to her, and create less of a burden, so I don't know why…"
"That's your problem right there."
Sherlock stopped in his steps and turned to John. "What do you mean?"
"You told her that her moving to Baker Street would be logical, and convenient?"
"Yes."
"And you didn't tell her that you wanted her to be there, and give her an emotional reason?"
"Well, of course I want her here- why would I ask if I didn't want her here?"
"But you didn't tell her that?"
"No," he said; as he sat down in his chair across from John, steepling his hands under his chin as he kept his gaze on his friend. "I don't understand why. Logical reasoning makes the most sense…"
"And feelings should just be assumed?"
"John, I don't assume anything, I deduce. Though, I suppose it would be assuming for someone like you, or Molly."
"It doesn't work like that though, Sherlock. You can give all the logical reasons you want, but it won't change. You can't just assume someone's feelings." He paused for a moment, and then continued. "She has told you that she loves you, yes?"
Sherlock tensed for a second, and then closed his eyes, sighing softly- "on more than one occasion."
"And did you know that she loves you before she said it?"
"I hadn't thought about it, but it was clearly obvious that she cared for me…"
"But did you know?"
"Well, no, I didn't have the evidence to make that final decision, I could have deduced it out if I tried, and I probably would have been right…"
Then it clicked- John knew that it was the only way to really discuss matters of feelings with Sherlock, to use scientific reasoning to get him to understand. Molly could do all she wanted for him, and he could assume all that she felt about him, but there was always things that Molly said that took him aback; there were always things he had never expected her to say, and therefore did not have the evidence to prove until the words fell from her mouth. This was the same case with those three words, he wasn't expecting them the first time she said it, but it was confirmed when she did.
And that was the key to feelings- you could look for hard evidence all you wanted, and make your deductions, but emotions aren't tangible. Expressing them was the only way to fully prove them.
"And you love her," John stated, smiling, folding his hands in his lap as he kept his eyes on Sherlock.
It broke Sherlock's train of thought; he opened his eyes and moved his hands down into his lap. "Sorry?"
"You love her- I know we've just discussed expressing feelings are proof, but I know you do."
He began to get defensive, and would try to hopelessly defend himself, but John wasn't an idiot. "John, don't be ridiculous, you know I don't think about-"
"Oh, bollocks, Sherlock, I knew it the second I saw you approach her after I shot Moran, and then I knew when you screwed up with her and acted strange for months, and then it was pretty clear when I saw you with her at my wedding. You didn't even stir around Irene Adler," and then he coughed, "who the first time you met her she was naked. And so I knew that just being," he waved his hand, "physically attracted to her wouldn't phase you."
"Plus, I know these kinds of things better than you," John continued, a smug expression crossing his face. "I'm a married man, I get this stuff." He was giving himself a lot credit.
"Please, John, how many failed relationships have you been through to be able to figure that out?"
Sherlock wasn't denying it now. "More than you have, much more than you, and so I think I've got the upper hand on this one."
When Sherlock said nothing, John spoke up again.
"And so you love her then?"
And with this, a knock was heard at the door.