For the sake of simplicity, and not typing everything everyone already knows, let us assume this occurs after the Empty Hearse, but without Sherlock meeting Tom. I have not seen the final two episodes yet, but I am going to try and remain as true to cannon as I can.

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Sherlock was lying on his sofa in 221 B Baker Street. He hadn't bothered to get dressed, apart from throwing a robe on over his jimjams. John was at work, and hadn't really spoken with Sherlock since he had been back. Mrs. Hudson was out. Mycroft was cross with Sherlock again, so calling him would be a waste of time and air. Sherlock sighed as his arm swung gently off the couch. He felt bored, but there was another emotion. Loneliness? Depression? Sentiment? Perhaps a mixture of all three. "Bored," he mumbled as he grabbed his mobile from the coffee table. His tea had long gone cold. He looked at the time, "11:30. John is at work." That didn't stop him from typing out a text.

11:32

Bored.

SH

A few minutes passed before he felt his phone vibrate.

11:35

I am working Sherlock.

JW

11:36

Dinner?

SH

11:38

No. I have plans with Mary tonight. To redo what you interrupted. No, you cannot come.

JW

Sherlock groaned before bringing his hands together and placing the tips of his fingers under his chin. Loneliness, that's what this is. Just as he retreated to his mind palace, his phone vibrated against his chest. "Sherlock? It's Lestrade. We have a case," Lestrade's voice carried through the phone. After agreeing to meet Scotland Yard around 2, he hung up the phone. He checked the time again, 11:47. "Molly will be going to lunch at 12:15. I shall surprise her," he said as he leapt from the sofa.

He entered his bedroom and pulled out black trousers and a deep purple dress shirt. After donning his coat, turning up the collar, and tying his scarf around his neck, he walked outside and hailed a cab. "Saint Bart's, quick as you can," he said as he shifted into the back seat. At 12:10 Sherlock walked into the cafeteria. He situated himself at a nearby table facing the door and waited. At 12:17, Molly walked in. He watched as she glanced around the room, looking for someone she knew. Her face lit up when she saw Sherlock. Nearly running to him, she stopped next to him. He motioned to the seat across from his own, "Please join me Molly." Eagerly she took a seat, placing her right hand on top of her left on the table, "Hello Sherlock. What are you doing here?" He gave her a smile that didn't quite reach his eyes, "I came to spend time with you Molly. Without your help, none of what happened would have been possible. I did mean to phone, but I had to be sure Moriarty's friends wouldn't find out." He stared at her intently.

"It wasn't a big deal really. The hardest part was keeping it from John. Especially at the funeral. You know, Mycroft wouldn't let me speak at it. Thought I wouldn't be able to keep the façade up. We filmed it though, for you. Thought you would like to see who all attended. Your parents weren't there. They couldn't bring themselves to go." Sherlock rested his head on the tips of his fingers. "I would like that Molly Hooper. Shall we meet tonight?" Molly fidgeted slightly, which caused Sherlock to become fixated on her. "Sure. Let me just text Tom," she said as she dug into her left pocket looking for her mobile. "Tom," he enquired, one eyebrow slightly raised. Molly jumped at the question and turned red. "Oh, um well," she stammered as she held out her left hand. "Ah, well, I hope you'll be happy Molly," he said casually. "Tom said it is fine Sherlock. How does somewhere between 7 and 7:30 sound," Molly said, hastening to change the subject. "That will be brilliant," he said standing up. "See you then Molly."

Sherlock arrived at the crime scene. "It is too quiet here. Where is Anderson," he asked glancing about. "Anderson had a moderate breakdown once you jumped. We had to let him go," Lestrade said his breathing uneven from having to jog to keep up with Sherlock, "Where is John?" Sherlock neglected to answer the question as he began going over the body.

The corpse was lying face down on the sidewalk in the ally. "From Cardiff, recently arrived in London, probably this morning. Happily married lawyer. Appears to have been poisoned with rat poison. Probably from a former client. I would go and look at his past cases and question anyone who lost their case," he rambled off while standing up and straightening his jacket. Lestrade nodded and looked over the body of a 40-something year old man in a suit. "Now, Detective Inspector, I must be going," Sherlock said as he tied his scarf and walked away.

As he entered Baker Street, Mrs. Hudson greeted him with tea, "Not bored are you Sherlock?" Her eyes were full of concern. "Not today Mrs. Hudson," he replied as he headed upstairs. The flat was quiet and empty. All of John's belongings had been removed by now. Sherlock smirked as he glanced around; Mrs. Hudson had dusted while he was away.

Sherlock spent the next few hours composing a violin piece. Even if he weren't invited to the wedding, the least he could do was write them a complex yet beautiful piece of music. At 6:30, Sherlock started pacing, "Arriving at 7 would give me time before Tom got there, but 7:30 would make us arrive together. If I arrive at 7:15 though, I will have a few moments to get settled and ask Molly the proper etiquette with Tom." Sherlock looked at his phone. "15 minutes and then I'll leave." He headed for the bathroom to fix himself up before heading out. At 6:45 he hailed a cab. After giving Molly's address, he watched out the window. When the cabbie stopped, Sherlock paid him and glanced at the time: 7:10. "Drat," he mumbled as he found a park bench nearby to wait on. At precisely 7:15 he knocked on Molly's door.

He had never seen her in plain clothes before. He smiled a smile that went all the way to his eyes. "Evening Molly. May I," he inquired. Molly showed him in before quickly shutting the door, "We don't have much time Sherlock. I have a favor to ask you." Sherlock spun around and began studying Molly. "It's Tom. Something doesn't feel right. Could you please, deduce him tonight and let me know if everything is alright?" He stiffened, "You're asking me to pick apart your fiancé? Of course I will." Molly gave him a relieved smile before showing him to the sitting room. They sat in silence until Tom walked in. Sherlock stood as he entered the room, "Evening Tom. I am Sherlock Holmes." He extended his hand for a handshake. Tom gripped it tightly, "Molly told me all about you. I must say I was puzzled by you. The first time she mentioned you, she said you were dead, but here you are in my sitting room." Sherlock glanced to Molly, and she thought she saw worry in his eyes, "Yes, well, had to disappear for a while. Things to do."

The both sat on the couch, with Molly in the middle. Tom wrapped a protective arm around her. "Let's get started shall we," she said walking over to the telly and putting in the DVD. For the next hour, no one spoke. Molly would occasionally rub Sherlock's arm when he would shift uncomfortably. At the end of the film, Tom got up and gathered the dishes. As soon as he rounded the corner, Sherlock whispered into Molly's ear, "I don't care how you do it, but be at Baker Street tonight. Your life may depend on it Molly. Promise me." Molly looked at him shocked before her quivering voice responded, "I promise." When Tom reentered the room Sherlock stood up to leave. "It is getting late, I must get home. Thank you for showing me this; although I will be speaking with Mycroft about his awful speech," Sherlock said nodding at Tom. "I'll walk you out," Molly said standing up. She placed a kiss on Tom's cheek before leading Sherlock out. As they passed the railing in the hall, Sherlock quickly untied his scarf and left it on the banister. "Thank you Molly," he said as he shook her hand. He spun on his heel and left.

Molly shut the door and noticed Sherlock's scarf. Sighing she headed back into the sitting room. "Ready for bed Tom," she questioned as she turned off the telly. "Yes of course," Tom said as he entered the hallway. "Is this Sherlock's," Tom re-entered the room holding the scarf. "Oh my gosh yes. I need to take that to him. He will be utterly a wreck without it." She held out her hand for the scarf, but Tom didn't give it to her, "Can't it wait until tomorrow?" Molly shook her head, "No. He will be here looking for it later. He doesn't get sentiment with people, just objects." Tom's fist clenched around the scarf before handing it to her, "Hurry back."

Molly hailed a cab, not wanting to take her car, just in case Tom followed, which she was certain he would. She asked the cabbie to take a less direct route to Baker Street, and to park around the corner. Once they arrived she pulled herself out of the cab and bumped into Lestrade, "Don't be alarmed Molly. I am going to guide you to 221 B. Sherlock told me Tom may show up here. Scotland Yard is stationed and waiting in case something happens." The quietness in his voice told her that she was in danger. As they reached Sherlock's door, Lestrade said a little louder than normal, "Good to see you Molly. I'll see you in the morgue later this week." He then continued to walk down the street. Molly sighed and rang the bell.

Mrs. Hudson opened the door, "Molly dear, whatever are you doing here so late?" She stood aside so Molly could enter into the foyer. "Sherlock asked me to come." Mrs. Hudson stared at her in disbelief. "Sherlock," Mrs. Hudson called up the stairs. His silhouette appeared at the top of the stairs, "Molly, please come up here. John and Mary are on their way. Hope you don't mind." She breathed a sigh of relief, "Not all." Once she entered Sherlock's flat she gingerly sat on his sofa, "Tell me." Sherlock was pacing, "I have reason to believe that Tom is actually Theodore O'Malloy, believed murderer of 3 women, all matching your similar description and personality type. There were scars on his knuckles that were the shape of teeth. O'Malloy escaped the jail before they could convict him and hasn't been seen since. Tom has obviously had some facial work done. Notably a hairline, eye lift, and a nose job." Sherlock glanced to Molly and watched as she slid her engagement ring off. She had learned to trust Sherlock, and she couldn't deny that something was off about Tom anyway. John and Mary suddenly appeared in the doorway. Mary rushed to Molly and hugged her.

"Why did you need us," John asked quietly as he and Sherlock watched out the window for Tom. "I don't understand emotions very well. I need help in comforting Molly," he glanced over his shoulder and felt a pang in his chest as Molly began to cry. John couldn't resist, "You care for her. Don't you?" Sherlock scoffed at his remark, "Please John, you know me better than that." John shook his head, "See, that's where you're wrong. You have been gone 2 years. Even the great Sherlock Holmes can change." Before Sherlock could respond, they saw Tom get out of a cab. "He is here Molly. John, take my phone. If things get ugly, hit send. It is a message to Lestrade."

A few minutes later, Mrs. Hudson showed Tom in. Mary held Molly closer and Sherlock stood at the perfect distance between the two so he could jump in and defend the girls if necessary. John stood behind Mary and Molly, the phone hidden in his pocket. "Molly. I thought you were just dropping-" he stopped when he saw her ring on the coffee table. His face turned a shade of red and he headed towards Molly. Sherlock intercepted him by crashing into his side and knocking Tom to the ground. John hit send and raced to help his friend as Mary pulled Molly into the kitchen. Sherlock knocked Tom down again when he tried to get up and John leapt in to restrain him as Lestrade and his men burst in. Theodore was arrested and drug away to the station. Sherlock and Molly said good night to John and Mary and then sat together on the sofa.

They were quiet for a while before Sherlock said, "Shall I call you a cab?" Just as he said this, Mrs. Hudson smacked his arm. "Ask her to stay Sherlock. She shouldn't be alone." Sherlock nodded, knowing Mrs. Hudson would know how this felt more than anyone. "Molly, will you stay? You can have my room for the time being and I will sleep in John's room." He held out his hand for Molly, and led her to his room. Sherlock didn't see it, but Molly did: as they walked but Mrs. Hudson gave a knowing smile to them before sighing.

"This is the um, closet. Feel free to use a shirt so you don't have to sleep in your clothes. We can go and get you some of your clothes tomorrow, and your car. Lestrade will be telling the hospital you won't be in for a while, at least until you are ready," he said as he shoved his hands in his pockets. His palms were sweating, and he couldn't be sure as to why. "Thank you Sherlock. This is really sweet of you to do for me," Molly said as she sat on his bed. "Yes, well. If you need me, I'll just be upstairs." With that, he left Molly alone in the room. She grabbed a red button down shirt out of the closet and slipped into it, it fell half way down her thighs. She had just finished buttoning it when Sherlock opened the door. He was holding a cup of tea. "Thought you might need this," he said. The words caught in his throat a bit as he looked her over. "Mrs. Hudson told you to bring it to me, didn't she," Molly asked taking the cup from Sherlock. "Yes, she seemed to think it would be a good idea," he shifted nervously. "Thank you Sherlock, good night." "Good night Molly." He turned and headed up the stairs, for some reason, his pants felt a little tighter. Molly grabbed the collar of his shirt she was wearing and breathed in his scent. Sighing she flopped onto the bed, and was surrounded in the scent she had only dreamt about. Curling up with the pillow, it was the best sleep she had received since Sherlock had jumped from the building.

XXX

I can't guarantee all the chapters will be as long as this one, but when you are cleaning at work and your brain writes a fanfiction, you just have to include all the details.