He talked to her every once in a while. He visited her flat even less, but during the two years that he was away, Sherlock Holmes was still in contact with Molly Hooper. At times it was the only thing that kept him going. He had experienced torture and loneliness and hunger and exhaustion and experiences that made even him, the great Sherlock Holmes, want to give up. But then a man in traditional garb would pass him on the street and discreetly hand him a phone with one number programmed into it. He would quickly find a safe place, one where he would not be overheard, and he would dial, most times not being able to contain the smile on his face as he anticipated her voice. And never being able to contain the laugh that eventually erupted from him when she tried to make a joke to cheer him up.
It was during one of these phone calls that he originally deduced something oh so important. She was bubblier than usual, more cheerful. Molly had always been cheerful but the wear and tear of the past few years had set her to a darker place, one where she was always on edge and mourning the fake loss of her consulting detective. But this time was different. He heard a spark in her voice that was characteristic of the old Molly, the one that made him admittedly fall for her despite his best efforts.
He didn't want to believe the deduction he made as soon as he heard it, but it couldn't be lost on him. She had a new boyfriend.
He wasn't that much concerned over this new development. Molly had boyfriends and many of her relationships didn't last very long. The men were never good enough for her. Though he still thought about this new man when he lied awake at night, wondering if he treated her how she deserved, and hoping that at least she was happy.
It wasn't until he paid her a visit, stumbling into her flat at two in the morning with a gash in his side and the smell of tobacco lacing his breath, that he realized the depths of this new character in Molly's life. She did well to try and hide the evidence, although he wasn't sure why she would. In the back of his mind, he hoped that it was because part of her was still waiting for him. However, he still noticed the two different mugs laying on her countertop, the extra books on her shelf that would never belong to her, the buzzing of her phone as she received yet another text message.
She didn't mention it. So neither did he. He slept on her sofa that night while she sat on the floor beside his head, stroking his hair and telling him about how John was doing. She breathed life back into him despite his fatigue, the now stitched up cut, and his frustration in being away from Baker Street for so long. He listened and hoped that whatever was going on in her love life was over by the time he returned to London. He made a promise to himself shortly after the fall that when he came back things would change. He would be a better friend to John. He wouldn't criticize Lestrade and the Yard so much. He would tell Molly how he felt about her.
He woke up early the next morning to see her head rested beside his, her breath coming out in small puffs and blowing away the stray hairs from her eyes. He gently carried her to her bed, tucking the covers around her and gently kissing her forehead before heading out.
The next time he saw her was when he was back for good, catching her eyes in her locker mirror as he smirked at her shock.
"You're back," she said and then shook her head. "Obvious," she laughed lightly then and he did, too, taking two steps toward her and wrapping his arms around her, their two years spent in secrecy bringing them closer, closer to anyone Sherlock had ever been. "For good this time? I mean you did it. You defeated the network?" she asked into his shoulder, breathing in the tobacco and city air smell from his Belstaff.
He pulled back and looked at her. "Defeated. Derrotado. Poražen. Verslagen. Vaincu. Unterlegen. Sconfitto." She giggled gleefully as he took her hand and spun her in a circle. "And all thanks to you, Molly Hooper. I couldn't have done it without you."
"I'm sure Mycroft helped a little," she said through a smile and he shrugged noncommittally, one hand still in hers and the other on the small of her back.
"Maybe a little." A comfortable silence settled between them as they stood there staring at each other, their eyes assessing, almost as if to check if the other one was real.
Molly was the first to break the silence. "Have you seen John yet?"
"No. But I'm going there next."
"You came to see me first?"
"Well…" his eyes searched the room and a blush took over his cheeks without his permission. Molly grinned at the suddenly bashful detective. "Yes," he finally said and she nodded.
His deduction skills started to kick in then as he looked behind her, at pictures on her locker of herself and another man. He couldn't see it clearly enough to see the face but Sherlock knew that it had to be the boyfriend that she was still obviously with judging by the small amount of weight she gained since he last saw her, the extra bit of makeup that covered her face, and the way she was currently playing with her left ring finger.
He froze on the spot, his gaze going downward to see that thankfully, no, she wasn't wearing a ring. But the boyfriend had asked her to marry him. She just hadn't given an answer yet, thinking it over, testing to see how a ring would feel. There was still hope, he supposed. He assumed that she didn't say yes or no because of himself, maybe because she was waiting for him to return. His brain kicked into gear, formulating a plan to get her back. Or get her in the first place as he never actually had her as much as he liked to think that she was his pathologist.
"Right," he said and cleared his throat. "Best be off. I have a very important dinner to attend," he said and rushed out of the lab his coat billowing behind him. Molly eyes trailed after him thinking that it was just like old times.
Sherlock's lack of partner and his plan to spend time with Molly brought him to asking her to solve crimes with him. He enjoyed the day thoroughly, being graced with the presence of his pathologist. He figured it couldn't hurt, asking her out to dinner. But it was after the words leaved his mouth that he figured out she had said yes to her boyfriend's marriage proposal. He wondered why he didn't see it before, but he supposed he just didn't want it to be true. He had been desperately hoping that she had said no, that she had waited for Sherlock. But, no. He was too late and he supposed that in the end he fell into that category of not good enough for her and that perhaps it was for the best.
Sherlock met him a while later. Tom. A safer version of himself. Molly found another version of Sherlock, but Sherlock knew deep down that he would never find another version of Molly.
"Tell me about him," he said to her one day when he was in the lab. She looked up at him from her paperwork, her eyebrow arched.
"You probably know more about him than I do," she replied but then backtracked. "Not what I meant. I just mean that I know you've already deduced a lot about him."
"Are you happy?" he asked instead and she nodded.
"Very." His heart fell.
He spent time with her in the lab over the next several months, things not returning to normal but changing to a new normal, one where their conversations came easily and their time together meant more to Sherlock than anything else. Now, he stepped into the lab and approached her. "What are you doing here?" she asked him in an annoyed tone, one that made him take a step back and offer her a questioning look. "Sorry," she conceded. "Bit on edge."
"Yes. I saw your bitten fingernails and your shoulders tensing when you looked into your microscope." It was her turn to throw him a look. "Sorry. I told you I wouldn't do that anymore."
"Right," she replied and turned back to her samples. He stood awkwardly at the end of her the table before deciding to settle down beside her to look at another sample under the neighboring microscope.
"So what has you so tense?" he asked quietly and she managed a laugh.
"Do you really want to talk about this? Don't you have it deduced already?"
"No. You may find this surprising but you are sometimes a complete mystery to me, Molly Hooper." She didn't answer back and when he sat up he found her staring at him, biting her lip. "What?"
"You've changed."
He shrugged. "So have you."
She sighed heavily before turning to face him; he mirrored her actions, bringing them face to face. "Tom and I are just… he's just being… I didn't think it would be like this," she admitted and ran a hand through her hair. Now that she was sitting up he could see the bags under her eyes and the spark that was gone again, just like when he left.
"Like what?" he asked.
"He's just being so difficult. He got a job offer up North and he wants to take it which means I would have to go to but it's just not something I want to do. I dated him because I thought it would be safe and consistent and I thought that's what I wanted. But now he's leaving and I'm supposed to want to follow like when you…" she cut off suddenly, tearing her eyes away from him and busying herself with cleaning up her area.
He hung on her words, knowing where her sentence was going to lead. Like when he left. She would have followed, he knew that when he asked her to help him. "Anyway," she said now, "you don't care about any of that."
"Molly," he said, shocking himself as he didn't think about talking. It just came out. "I realize that you seek stability. You should know that I don't have plans of leaving. Not again." He gathered his scarf, wrapping it around his neck. "You deserve to be happy, Molly. And if you're unhappy with Tom then… well like I said, I'm not leaving. You've been pulling away lately and I assume that it's because of him. I'm afraid that if you marry Tom then I will no longer get to see you. We'll be strangers. And I know that I wouldn't be the only one unhappy about that. See you later."
Molly stood stock still and dumbstruck, trying desperately to decipher the detective's words.
"Nooooooo," laughed Molly as she handed a test tube to Sherlock and focused hard on not spilling it as her body shook from laughter. He laughed right along with her, his eyes crinkled at the corners. "You did not say that to Anderson. You didn't."
"Course I did," he replied as he stirred up the tube. They were standing in the kitchen in dressing gowns and goggles, spending their days off together.
"What did John do?"
"He wasn't there. He's been busy, you know, with the wedding and Mary and everything." He looked down at his samples, eyebrows furrowed together.
"Sherlock, how are you feeling about all of this?"
"All of what?"
"You know. John getting married."
"Oh you mean John getting married, Lestrade finally dating again, Anderson and Donovan having an affair, Mrs. Hudson having sexual relations with the man downstairs." He paused. "You and Tom."
"I actually mean just John moving out but okay. So what's wrong with all of that? Everyone's happy," commented Molly thoughtfully and followed Sherlock into the sitting room, sitting in John's chair.
"You're not happy," he said thoughtfully, expecting her to argue. But, she didn't, not in the slightest.
"This isn't about me. This is about you. Are you not happy?"
"It hardly matters."
"It does to me. You should know that you always have me, Sherlock. Always."
It was a few days later that Sherlock admitted his feelings for the first time, just not to Molly. "I love her, John," said Sherlock as he slumped against the cell wall, his head spinning and his speech slurred. John's stag night had not gone as planned and the mix of alcohol and Sherlock's depression about Molly's engagement was not good for the detective.
"Who are we talking about again?" said John having to focus on each syllable.
"Molly. My pathologist, of course. I love her. And she loves someone else. Tom."
"Tom," John nods in agreement.
"D'you know what she told me the other day?"
"Hm?"
"She said they were having lots of sex," he slurred and his cheeks turned even more red.
"She said that?" replied John with as much shock as he could muster up. Sherlock simply nodded. They were quiet for a beat.
"I could have lots of sex with Molly. I could do lots of things with Molly."
"You should tell her."
"She's engaged. Remember? Do keep up, John." At this point John dozed off on the floor and Sherlock sighed heavily from where he was in the bed. "My Molly," he mumbled before he himself fell off into sleep.
She walked into his hospital room, watching him sleep, however not very peacefully. He murmured something she couldn't make out and she placed a small book about bees on his bedside table. She sat down beside him, placing her small hand in his large one and this seemed to stir him out of his sleep.
"Please tell me you actually broke up with meat-dagger," he mumbled while playing with the empty space on her left ring finger.
"Yes. I actually broke up with him," she said and rolled her eyes, leaning forward in order to hear him better.
"Thank God for that."
"Why do you care so much?"
"I'm obviously in love with you Molly."
"You're obviously on mass amounts of pain killers right now."
"You don't believe me."
"Not exactly."
"Well it's true." He attempted to sit up, pointing his hand to the table. "Reach into that drawer over there. There's a black box. Open it." She did and saw a very beautiful engagement ring. It actually took her breath away.
"Is that what you used on Janine?" she asked.
"No. It's the one I was going to give you." She almost dropped the box, her hand flying to her chest and her breath coming in sharply.
"When did you get this?"
"When I was in France."
"That was a year and a half ago," she remembered. He had phoned her from France and said he was having a good day. Well now she knew why.
"Very good. Your deduction skills astound me," he said, his words comically slurred.
"You somehow managed to propose to me and insult me in the same meeting and I think that's a new record for you," she replied laughing softly and shaking her head, still staring at the ring.
"I'm not proposing. Not yet. It has to be proper. And seeing as how I have trouble getting up let alone getting on one knee, you may have to wait a bit."
"We've never even been on a date."
"We've been on several dates. You were engaged for most of them but that's hardly the point. Besides, dating is just a social construct meant for people to get to know each other. I know you. You know me. And this is a conversation I'd much rather have when I'm able to think straight." He winced in pain and pumped up his morphine slightly.
She stood up and grabbed his face, planting a kiss on his forehead. "Sherlock Holmes, you ridiculous man."
"Please stay," he whispered when she went to leave. She smiled but sat back down, grabbing his hand and squeezing softly.
Mycroft had a car waiting for him just outside the hospital, but he requested a stop. He had someone important to see. He knew this would be the last time that he would ever see Molly Hooper and his heart ached at the thought. He walked into the morgue and everything looked so normal- the metal tables, the various tools, and his pathologist, bent over a body, elbows deep in someone else's blood.
He cleared his throat, making her jump in the quiet room, but it got her attention. He didn't even have to say anything. She knew.
"You're leaving?"
"I have to. I'm sorry, Molly. I never meant for this to happen but I need you to listen to me."
"What's wrong? What do you need?" she demanded, now removing her gloves and stepping toward him.
"I just need you to listen." He looked away briefly before establishing full eye contact with her, not breaking it once. "You are… incredible. You were everything to me. You changed me into something I never thought I could be. I will always think of you. Always. Promise you'll never forget me?"
"Of course," she whispered, a tear now running down her face. He could tell that she knew what was coming, that he wasn't coming back, that he would be dead soon.
He walked over and wrapped his arms around her. "I don't know what to say," she said softly into his chest, her hand creeping up to feel his heart.
"You don't have to say anything."
"I really think the universe has something against us being together," she commented and he sighed.
"The universe is a concept. It does not have any decision making power and to think so…"
"Sherlock. Just shut up and hold me," she cut him off and he followed her orders.
"Watch over them. Over John and Mary and the baby and Mrs. Hudson and Lestrade. Keep them safe for me. And you, you go out and be happy. Promise me that, Molly."
"I promise," she found herself replying and reaching up to kiss him soundly on the mouth. He let himself become lost in her, his would-be-fiancée, if only for a moment. When she pulled away he rested her forehead against hers.
"If I could have this with anyone I would want it to be you. You are the only one, Molly Hooper."