A quick note: Thank you for all the nice comments and follows! This is only the second story I've published, and the first multi-chapter, so I know I have a lot to improve on with my writing (like for instance learning the correct British terms for things-I'm working on that) and I really appreciate the feedback! Thanks again for reading!

And without further ado here's the conclusion...

Staying true to his word, Sherlock ended up back in the hospital that same evening. He had taken care of his necessary errand before collapsing at Baker Street due to internal bleeding. John and Mary had been with him when the ambulance was called which had surprised Molly. She didn't even find out about it until the following morning when Sherlock texted her from his hospital bed. She tried calling John to get the details, but he wouldn't answer his mobile.

Molly visited Sherlock as often as she could. The ordeal had restored their friendship, but Molly noticed something was now wrong with John and Mary. She could only decipher that a huge argument had taken place that night. They barely spoke in each other's presence and the air was thick with tension. Sherlock wouldn't say what had happened between them, only that everything had gone to his satisfaction and that he would tell Molly when they had sorted it out. Apparently, he was leaving it up to John and Mary to fix things.

This time Sherlock stayed in the hospital until he was released. The doctors and nurses had naturally been furious with him for running off and he was kept under strict surveillance. Sherlock insisted that he had acted alone, which thankfully left Molly free from suspicion.

Sherlock returned to Baker Street and for the next few months life returned remarkably back to normal. While he was still weak and recovering, Sherlock only took cases "less than a six" that didn't require him to leave the flat. Molly visited several times a week offering assistance with the cases and often brought him the leftover results of her Bart's experiments with body parts to help with his boredom. John was at Baker Street even more often than Molly and usually seemed distracted and irritable. When Molly tried to ask about Mary, she only received curt, one-worded answers. No matter what John said everything obviously was not "fine".

One day after being frustrated by John's non-answers, Molly decided to visit Mary and see if she could get her side of the story. On a gray and dreary day, she showed up at the Watson's flat unannounced and was received with a wide-eyed look from Mary. She looked shocked as if Molly was the last person she expected to see. After the initial surprise, Mary warmed up and let Molly in the door cheerfully. They shared a pleasant conversation about unrelated topics over tea and biscuits and gradually the anxiety on Mary's face diminished. Mary seemed pleased to have someone to talk to, although Molly could tell that Mary was holding onto a secret. It looked as though several times she wanted to tell Molly something before stopping herself and changing the subject. Molly couldn't imagine what was going on between her and John that would have caused this tension. Their wedding had been beautiful, albeit for the attempted murder of Major Sholto. She had seen a couple that was obviously so in love and meant to be together. How quickly things had changed.

Feeling emboldened after their conversation as she was leaving, Molly asked Mary directly if there was anything she could do to help them. It was hard to read Mary, but there was a sense of worry in her eyes. Molly's heart went out to her and she gave her a hug. Mary hadn't exactly returned the embrace, but she smiled and thanked Molly for her concern. Once Molly was outside and nearly reached the street, Mary ran after her.

"It's my fault. I'm not sure that John will ever forgive me. I'm not sure you would forgive me if you knew the truth, Molly. But at the same time, I did something to protect my family," she paused and rubbed her rounded belly. "I don't regret that at all. But now I don't know what's going to happen. If only he hadn't…" She shook her head and didn't say another word.

Molly had been baffled by this cryptic answer. Why did Mary include her in it? What did she need to protect her family from? She was now more confused than ever about what had transpired that night.

When his strength returned after a few weeks, Sherlock and John were back to their usual routine of wandering around London solving cases and visiting Scotland Yard and Molly saw him less. Instead, she spent her weekly Baker Street visits with Mrs. Hudson sharing pots of tea, learning new baking skills, and getting caught up on the neighborhood gossip.

Sometimes weeks would pass in which Molly didn't see Sherlock at all and their communication was carried out via late night texts. Other times, mostly when he was between cases, she saw him quite regularly. He would spend long hours at the Bart's lab and even some nights at her flat. Some nights he stayed over and slept on her couch, other nights he left after she fell asleep. There was little physical contact between them. The night they shared on the couch together several weeks ago had become a distant memory. The air still felt charged with electricity whenever they were together, but neither acted on it. Molly felt like Sherlock was holding back, like he was waiting for something. What that something was she didn't know. Technically, he was still working on the Magnussen case, although it had stalled. Molly figured that something related to the case was the reason for his hesitance to become more involved with her. It felt like they were in a momentary purgatory, stuck between what had happened and what could potentially.

Sherlock obviously enjoyed his time at Molly's flat or she knew he wouldn't spend so much time there. They still had an easy relationship and talked for hours at a time, but Molly didn't feel that she could share her feelings with him quite yet. She had been so prepared and had planned what she was going to say, but when things had been turned upside-down her plans had been pushed aside. But now the holidays were quickly approaching and Molly felt that perhaps her chance would finally come.

The chance did not come.

It was Christmas Day and Molly was once again spending it alone. At least this year she wasn't spending it at the morgue.

Her mother had invited her to spend the day with her family, but Molly just felt like she would be an intruder. After her father passed away, her mother had remarried and moved to northern England. It wasn't the ends of the earth, but it might as well have been. Her mother was now busy raising a new family, as her husband had two teenage children from a previous marriage. It was a family that Molly didn't feel a part of. They were great kids and Molly enjoyed spending time with them, but she didn't ever feel that any of it was hers. She didn't belong.

Meena had also invited Molly over to her family's Christmas dinner, as she did every year, but Molly had politely declined. Christmas was a time for being with loved ones and she would rather be on her own than with someone else's family.

What Molly really had wanted was to spend the day with Sherlock. However, he was not at Baker Street, but instead had decided to visit his parents and had brought John and Mary with him. Molly had found it odd. In all the years she had known him, she had never heard of Sherlock spending time at his parents' voluntarily. He had mumbled something about fixing a marriage, but when Molly asked him about it he changed the subject. Sherlock was not the traditional sort of person when it came to holidays. Something was unusual about the way he had suddenly decided go off to the countryside. Molly thought maybe he would invite her knowing that she wanted to meet his parents and that otherwise she would be spending it alone. However, the topic was not mentioned again. She had tried not to be disappointed, but she couldn't help it.

Molly comforted herself with her favorite Christmas movies and by baking cookies. With her flat smelling like cinnamon and Toby curled up next to her, she came to the conclusion that it wasn't such a bad way to spend the day. In the evening, she had a long conversation on the phone with her mother. It helped to fill the hole in her heart, although the sound of laughter in the background only reminded her of the loneliness. Still, she had people to love even if they weren't near her at the moment and that was more than some people had.

Halfway through It's a Wonderful Life, her mobile chirped. She looked at the clock and saw it was just after midnight. With bleary eyes, she looked at the screen wondering who would be contacting her so late on Christmas. It was a text from Mycroft: My brother requests your immediate presence at Baker Street. - M. Holmes

Molly couldn't help but feel worry. For Mycroft to text her, it must be something major. The only times he had contacted her previously were regarding plans for Sherlock's faked death.

When the cab pulled up to 221B, Molly could tell something was indeed wrong. There were two armed guards standing by the door and police cars lining the street. She nervously approached the building.

"I'm Molly Hooper, here to see Sherlock." She tried not to let her voice waiver. One of the men spoke her name into his radio. The person on the other end must have given approval, because she was let in the door. Molly ran up the stairs as quickly as possible. Her heart was beating so fast she thought she would pass out. What kind of trouble was he in this time?

There was another guard standing outside of Sherlock's door. He nodded and let her in.

Sherlock and Mycroft were both standing alertly, like they had been pacing around the room and stopped upon her entrance.

"What's going on?" She asked, looking from one brother to the other.

Mycroft pointed to Sherlock's chair with his umbrella.

"Have a seat, Miss Hooper."

She sat down not knowing what else to do. Sherlock was standing by the fireplace. His expression was unreadable. He had not taken his eyes off of her since she had entered the room.

No one spoke. Mycroft was looking at Sherlock as if he was waiting for him to speak first. When he didn't, Mycroft sighed and began to put on his coat.

"My brother has something to tell you, Miss Hooper, that may come as a shock to you. I trust that you'll keep this information to yourself as you have done in the past. I will be waiting downstairs."

Mycroft left the room. Sherlock remained unmoved, but he now wouldn't look at her.

"Sherlock?" She asked quietly.

With a deep breath, he began walking around the room aimlessly, before finally grabbing the footstool and bringing it over so it was positioned directly in front of her. He sat down on it and took her hand with both of his.

"Molly, tonight I did something wrong. I don't regret it. It was done to protect my friends, but it has gotten me in trouble with the law."

Molly didn't know how to respond so he continued, not dropping his gaze at her for an instant.

"I killed someone. Charles August Magnussen to be exact. I did it to protect Mary and John."

"Mary and John?"

Sherlock nodded and proceeded to tell her everything about the night he was shot, Leinster Gardens, and Magnussen's mind palace.

Molly couldn't believe it. It seemed too unreal. Mary was a former assassin? She shot Sherlock?

"If I didn't destroy Magnussen, he would have destroyed Mary and subsequently John. I miscalculated his abilities. I was left with only one choice. It was either that or Mary goes to prison."

Molly felt her eyes tear up at the sacrifice Sherlock had made for his friends and the consequences he would now be facing. It was at the same time heroic and stupid. Sherlock was a murderer. Whether he had done it for Mary and John or not, he still killed someone and there would be punishment. He had acted impulsively and now…

"What happens now?"

Sherlock released her hand and started to pace around the room.

"Well, as you've seen, I am under house arrest for the time being. In a few days, I will be heading off to Europe for an undercover mission. Mycroft has to get approval, but it appears that I will be able to avoid prison."

He stopped in his tracks and once again came over to sit in front of her.

"Molly, I don't plan on returning. I'm not going to lie to you. I can't…" He bowed his head, fighting back tears. "Molly, this is the last time I will see you."

Molly stood up and released her hand from his grip.

"No…No…You don't mean that. I don't believe you."

"Molly…"

"No, Sherlock. This is part of some crazy plan. You're trying to throw me off."

"I only wish that were true…"

"You wouldn't do this to me. Not after everything…" Molly didn't care if she was in denial. She refused to believe that this was now their reality.

"Molly, please believe me."

"No, I won't." She felt her eyes fill with tears and headed to the door. "I can't deal with this. I need to leave."

"Molly, please don't go. Not like this." He came over to her, pleading with his eyes.

She gave a pained, forced smile. "I will see you again, Sherlock." She marched out the door without looking back.

Mycroft was standing outside, smoking a cigarette.

"I assume he's told you everything."

"Yes." She began pacing on the sidewalk nervously.

He took a puff and watched her. "I know you'll be discreet, Miss Hooper. You've proven yourself to be a reliable…friend to Sherlock. I see that you're angry and I don't blame you. My brother has gotten himself into quite a mess."

Molly stopped and took a deep breath. "Mycroft, I don't believe you or Sherlock. I won't believe that you would send him off on some death mission. I know you love your brother, no matter what you might say."

"You deduction skills are improving I see, but I must send Sherlock on this mission. It's the only choice I have." He flicked the ash off of his cigarette and paused, looking at Molly carefully.

"I see the way my brother cares for you, Miss Hooper. I've seen it for a long time. At first, I must admit I thought him foolish. I've never felt that caring is an advantage, especially for a person like Sherlock. It only gets in the way of his extraordinary gifts. But you have proven yourself to be a worthy partner for him. Normally I would say happiness is irrelevant, but he has seemed to be…content lately. I've watched him go through difficult times and have had to be the one to pull him out of it. Since you've entered his life, he's changed. Despite the occurrence a few months ago that he insisted was for a case, I don't see him returning to those bad habits now that he has you. Although I suppose now that it doesn't matter…"

"Mycroft, do you believe that some people are meant to be together?"

He coughed. "I try not to worry myself with such matters."

"It's like…" she struggled with how to explain what she was feeling, "you know how in chemistry, certain atoms naturally bond with each other. It just happens. It's nature. Maybe people are like that too. I feel that Sherlock and I just…fit together and things have finally started working for us. It finally felt like we could be together, the way we were supposed to be and then everything went crazy. I just refuse to believe it ends like this. I can't. I won't."

Mycroft looked unsure how to respond.

"Miss H-Molly, I wish I could assist you in some way. I do try to look after my brother. I wish there was another way, but I think it would be crueler to let him sit in a jail cell."

He took another drag of the cigarette and pointed to a car waiting in front of the building.

"Please allow my driver to take you home." He looked at her sympathetically. "I'm sorry, Molly."

Molly got into the car, worried that she was wrong. What if this was the last time she would see him?

No, she refused to believe it. It hurt too much. Besides, something deep within her told her that this was not the end and if there was one thing she had learned it was that she should always trust her instinct.

The day of Sherlock's departure arrived. Molly tried not to let her mind dwell on it. She was grateful to be at work and have a distraction. John and Mary were going to the airport to see him off along with Mycroft. She made John promise to tell her everything that was said. Although she was nervous, she still trusted her gut.

In the afternoon, she wandered into the staff room, where much to her annoyance someone had left the telly on. As she walked over to turn it off, the screen suddenly flickered and a familiar face appeared. A face she hadn't wanted to see ever again.

"Did you miss me?"

No.

It couldn't be.

Moriarty.

She had seen Jim's corpse. She had handled it herself. The back of his head had been shot off. His blood had covered her hands. He was dead.

This had to be the work of someone else. But who?

Suddenly the flashing image and cartoon-like voice were gone and the normal talk show resumed. After being momentarily paralyzed, Molly wandered absent-mindedly back to the empty and darkened lab, trying to make sense of the situation in her mind. Was it someone connected to Moriarty? Did they know her secret about helping Sherlock? Would they come after her? The timing of it could not a coincidence. Someone knew Sherlock was leaving at this very moment. Was this their way of keeping him in London?

All of these questions were circling in her mind when suddenly the door to the lab burst open without warning breaking her out of her reverie. The light of the hallway revealed the outline of the familiar tall and curly-haired silhouette. He stood still for a minute letting his eyes adjust to the light before finally spotting her.

He strode towards her with his coat sweeping around him. When he reached her, he wrapped his long arms around her shoulders and crushed her against his body.

After a stunned second, she put her arms inside his coat wrapping them around his warm middle, savoring the feeling of his body.

It didn't matter what was happening. She had him back.

"Molly," he whispered her name into her hair, not letting go an inch. "You're all right."

Molly had no idea how much time passed before they pulled apart.

"I'm sorry, Molly. I'm sorry about acting without you. I'm sorry for not considering your feelings. I'm sorry for being an idiot and getting myself into this mess. I'm sorry for everything."

"I'm sorry too. About the other night…"

"You don't need to apologize. You were right. How did you know I would be coming back?"

"Don't you know I'm always right, Sherlock?" Molly couldn't help teasing despite the circumstance.

He smirked. "I think I'll need you to remind me everyday."

"Everyday?" she asked, raising her eyebrows.

"Unfortunately, you're stuck with me, Molly. England needs me. And I need you."

This was the second time he had said that three-letter word in this very room. The first time he was planning his death. This time...

"Are you back for good?"

"Yes. You're not getting rid of me now." He smiled before turning serious once again. "Mycroft figured I would last six months, but I was planning on lasting a lot longer than that. I was planning to come back to you. I just wanted to prepare you in case…I didn't. Nothing was guaranteed."

"I'm sorry I was so angry that night. It's only because I love you and I couldn't bare the thought that it was the last time I was going to see you. I just knew deep down that there was more in store for us."

"Love? You love me?"

"Of course. I've loved you for so long, since that first day we worked together. I've wanted to tell you for a long time, but there's been so many obstacles. First, you fake your death and leave for two years. Then I tried to move on and got engaged, only to realize I was still in love with you when you returned. Then this whole mess with the Magnussen case and you getting shot…I wish you would've realized when I told you that one Christmas…"

"You mean when you wrote 'Love, Molly' you meant it?"

Molly smiled. "Yes. Of course I did, you bugger. If you hadn't been so focused on the fact that I had some mystery boyfriend, you might have seen it."

"I'll always regret what I said to you that night, Molly. God, I was so sure there was someone, it blinded me. When you walked in with your hair…and that dress…I just…"

"What you didn't think someone would ever dress up for you and give you gifts?"

"No."

"Sherlock, you may be a difficult bastard at times, but you're not unlovable. You're flawed, and have a bit of an ego. You talk too much at times, and have a temper…."

"Hey…"

"…but you're too hard on yourself. You are as worthy of love as anyone."

"I hope I can feel worthy of you someday. I feel like I have a lot to make up to you. In the meantime, will you accept my love, Molly?"

"You love me?"

"Of course, isn't it obvious?"

"I…"

"Molly, you see me more clearly than anyone."

"I know we have something, I just didn't know exactly what you felt."

"Perhaps we need to work on your deduction skills. Notice my pupils."

Molly stared into his eyes; the darkness nearly consumed the blue-green of his irises. "They're dilated."

"Correct. Now take my pulse." He had leaned in and spoke close to her ear, sending chills down her spine.

Molly swallowed and lifted two fingers to his neck. "Elevated." She could have been answering for her own pulse as well.

"Correct." Sherlock's voice had dropped so low that he was nearly growling with desire. Molly was almost trembling with anticipation.

After what felt like an infinity, he slowly brought his hands to the sides of her head, cradling it gently with his long fingers. His movements were so slow and delicate that Molly thought she would be driven mad by her want for his touch. Just when she felt herself on the brink, he lowered his mouth to hers and kissed her with a passion and intensity that would have made her gasp if she had been able to breathe. His lips were as soft as she had imagined, but the sensation caused by his mouth on hers was greater than anything she could have dreamt of. It felt like an electric current was surging through her veins. The kiss started slowly as if Sherlock was trying to savor every second and commit it to memory. Molly felt like she had left her physical body and was falling through a void in which she had no desire to land. Instinctively, she raised her arms to grab something to ground herself and her hands landed in his hair. She had fantasized for so long about running her fingers through the silky curls and allowed her hands to explore the tangles. She gently pulled at it, making him groan deep in his throat. This reaction she had caused excited her and made her want more. The kiss deepened as their tongues became involved. Moans and ragged breathing intensified and neither were no longer concerned about holding anything back. Molly felt the heat of Sherlock's lower body as they pressed into one another. He led her to the edge of the table. Neither had any desire to stop.

Just as Sherlock was about to lift Molly onto the table, a voice broke through the haze forcing them at last to part their lips.

"I do hate to interrupt, but let me remind you both that the country is in danger, in case you hadn't forgotten."

Mycroft had entered the room and was smirking at the two of them.

"Damn it," Sherlock muttered under his breath and leaned forward, pressing his forehead against Molly's. They were both breathing heavily.

"I trust, little brother, that you haven't forgotten the situation we are currently facing."

"Of course not." Sherlock pulled his head back with his eyes never leaving Molly's. "I needed to get my partner-in-crime."

"I can see that. Hello, Miss Hooper."

Molly nodded at him sheepishly, unable to hide a smile.

Mycroft's mobile rang breaking the awkward moment. He gave a sigh after looking at the screen and immediately left the room. Molly could hear him giving orders regarding the hacked television screens to the person on the other end. It suddenly brought to mind what was happening.

"Who's out there, Sherlock? Who's doing this?"

Sherlock smiled tenderly and took Molly's hand.

"I don't know, and I don't like not knowing. But we're going to find out. First, I think we must find Mike Stamford and let him know that you are not going to be working the rest of the day. Then we're solving a case and then…"

"Then?"

"Then we're having dinner." Sherlock raised an eyebrow and gave Molly a look that made her cheeks turn pink.

They strolled out of the lab hand-in-hand, ready to face whatever might come their way.

Together.

THE END