Thank you to everyone who enjoyed my last story. I hope you'll also enjoy this multi-chapter story. Looking forward to your reviews.

The Final Stand of Sherlock Homes and James Moriarty

Chapter One

"Molly sweetheart, whose shirt is this? It's not mine, and I've never seen it here before," Tom yelled from the bedroom.

"Oh, I think Sherlock might have left one behind when he was living here after we faked his death. I must have moved it when I was cleaning yesterday," I answered. The crisp white shirt in question popped to the forefront of my mind. I decided that I should keep to myself that I still wear the shirt to bed some nights. Probably best not to mention that I was wearing it the shirt when Sherlock left in the early morning hours two years ago as well.

I really need to stop wearing it. I should probably give the darn thing back to Sherlock now that he's "alive" again. I have moved on, and need to stop giving into these childish fantasies about him. I am in love with and engaged to Tom now. For once in my life I am happy. I shouldn't need the shirt to feel the comfort of knowing that Sherlock is still alive any longer. I am a grown woman, I shouldn't need a security blanket. However, if all of that is true why does the thought of giving the shirt back cause my heart to ache?

"How long did he stay here that he felt comfortable using your closet? Isn't that a bit intimate?" he asked as he walked back into the front room.

"He was here for about two weeks, but he put his things in my closet the moment he moved it. You'll understand once you meet him." Even as I said the words I realized I'm not sure that I want them to meet.

When it comes to Sherlock his words are capable of cutting to the bone. He doesn't understand boundaries, and being my fiancé may make Tom a bigger target for Sherlock's deductions. He loves knowing everything about everybody with just a glance and knowing that he's the superior being in the room. I don't want to know what he'll say about Tom. He was being nice when I saw him a couple days ago, but I know it can't last.

"I've got to head out for my dinner meeting. Are you sure you don't want to join me?"

"No, I've got a few things to finish up at work. Plus there is some paperwork that needs to be filled out now that Sherlock is 'alive' again. However, Mycroft said that he's clear it all up," I replied.

"What would need to be cleared up, and who is Mycroft?"

"Tom, my name is on the death certificate of a man who is still very much alive. I've helped to commit fraud. Mycroft is Mycroft Holmes, Sherlock's older brother. He works pretty high up in the government. Sherlock likes to say that Mycroft is the government," I couldn't help but chuckle at that last bit. I can even hear Sherlock saying that words in that voice he uses anytime he's talking about his brother, bored and dry.

"Was helping him really worth all this trouble you might be in now?" he questioned as he grabbed his coat.

"I understood what was at stake when I agreed to help him. I'd do it all over again today if he asked me to."

"He must be a really good friend then," he sounded angry about my friendship– if you could call it that – with Sherlock. That I would risk so much for him. "Well, I'm going to head out then. I'll see you later. Love you."

"I love you too," I responded as he leans down to kiss me before leaving.

I don't really having any paperwork pertaining to Sherlock to fill out down at Barts, Mycroft had taken care of everything already. I really couldn't sit through another one of Tom's business dinners though. I'm not good with conversation under the best of circumstances, and the fact that I spend my days cutting up dead bodies doesn't help matters. No one wants to hear about my job while they're trying to eat; no one ever really wants to hear about my job. The only person I know that has no qualms with conversations about corpses is Sherlock.

And of course Sherlock Holmes is the only subject that people really want to discuss with me once they've discovered my association with him. Before his resurrection the questions were always about why I believed in him. Now that he's alive again all they want to know is how we faked his death. No one seems to care about the things that really matter such as the fact that Richard Brook really was Moriarty and that Sherlock was cleared of any wrongdoing, or that Sherlock was protecting his friends when he faked his death. No all they care about are my motives and judgment. It seems like even Tom is questioning my decisions now.

Tom didn't even know me two years ago, so why is my association with Sherlock, my motives for helping him, all Tom seems to care about these past few days? I work with Sherlock and can't have Tom getting miffed every time I mention his name or they happen to see each other. Why is it that Sherlock can't help but to make my life difficult?

I decided that going to Bart's wasn't such a bad idea. I've always felt like myself at the morgue; my home away from home. The cold and sterile environment has always comforted me, which is strange since I love warmth and color. Being there would help me clear my mind and keep my sanity at bay. I have so many memories connected to Sherlock that are connected to working with him there, and while many of those memories are not happy ones, I always felt needed and content when working with him.

Maybe there's something wrong with me. I love Tom and I am happy, but with Sherlock back he's constantly in the forefront of my mind. Everywhere I turn there is some sort of memory associated with him. I'm sure they've always been there, but now they're staring at me in vivid color. I don't know what I'm supposed to do about it all. I'll go to Bart's and everything will be better; I'll get it all figured out.

I had just sat down at the microscope to check on a skin sample when Sherlock swept through the doors like he owned the place. It wasn't really surprising, some things would never change. Even as confused as I am right now it's nice to have him waltzing into my domain again. I missed this while he was gone, and was always looking up hopeful whenever my door opened.

"Oh, Molly, you're already here. I thought we were going to have to wait for you." My mobile starts ringing as he finished.

"Hello? Yes, Greg. I'm actually already here. Yes, Sherlock is here too, he just walked in. No, I won't let him push me around while we're waiting for you. Okay, we'll see you soon."

"Does he really think I'm going to push you around?" Sherlock asked looking puzzled.

"You have to admit you've done it in the past," I said getting up from my spot at the microscope. I can picture every moment that he ever demanded something of me, treated me like I wasn't really there, flirted with me to get whatever it was he wanted or needed at the time, and every time he pointed out everything wrong with whoever I was dating at the time.

"That was before, things have changed."

"Have they really changed that much?" I asked, unsure what could have happened in the past two years that would have changed him so drastically. I know that when I helped him fake his death I moved up in his little world, but even John who is his best friend has to deal with Sherlock's abysmal behavior. What makes me any different?

"Molly," was all he said in his impatient voice, the one that tells you that you're supposed to understand everything that he's saying. I don't know why, but the sound of his voice suddenly made me nervous. Just what I needed, to constantly be jumpy around him again.

"Tom found your shirt in my closet this evening," I don't know why I said it. I just needed something to say and it was the first thing to pop out. I really was going to end up a jumpy nervous mess around him again…uhh.

"That must have been awkward," he said with a hint of a smile. I think he was secretly pleased that I still have the shirt, that I kept that small piece of him around all these years. If I'm really honest with myself I guess that means I haven't really moved on as well as I thought I had.

"Well, yes, it was a bit. I told him you must have left it by accident when you were staying with me. He didn't make a big deal out of it, but seemed to think it was too intimate for a male friend to be so comfortable to put their things in my closet.

"Molly, I think we were a little more than friends for a little bit, weren't we?" I nodded in answer, knowing I was blushing. "Do I need to come by and fetch it later?"

"I don't know. I'm very unsure about what I should be doing."

"I know that I like to make people uncomfortable just because I can, but I want to be happy. You deserve all the happiness in the world Molly, and I don't want to get in the way."

"It's just…" I can't seem to finish my thought process, I'm not even sure what I meant to say in the first place.

"You know, you look better in the shirt than I ever did," he said with a sly smile that causes a tightening in my chest. I've only ever felt this way with him, and that scares me.

What was I doing letting him get to me again? Thinking about that night he left two years ago. Him kissing me goodbye, me wearing the shirt. Earlier that day he'd told me he didn't know when or if he'd ever be back in London. I figured that I would never be able to move on, Sherlock was everything that I measured every man I met against. Then one day Tom walked into my life, and everything changed.

"Why do you do that?" I stammered out the question. "You tell me you want me to be happy, but then you just have to go and say something like that to throw me off balance!" I said all this with my voice getting a little bit louder with each word as my anger grew.

"I'm sorry Molly. I just can't…I wasn't thinking."

Thankfully before I can respond DI Lestrade and Sargent Donovan came in. I was having trouble trying to process everything Sherlock was trying to say. It was all so confusing. I decided it would be better to focus on the other problems at hand instead.

"The body still hasn't arrived Greg," I said finally looking away from Sherlock.

"I don't know what could be keeping them. They left the scene with the body shortly after Sherlock, and well before me and Sally.

"I'll just check out back then; see if they're having trouble with something."

"I think I'll go with you. That is if you don't mind me accompanying you?" Sherlock asked, the confidence usually found in his voice was gone. I nodded in response.

As we started walking back to the ambulance dock I was sure I heard Sally asking Greg, "What the hell is going on with Dr. Hooper and the Freak?" I guess that means Sherlock was his normal self at the crime scene earlier. Which means things really haven't changed and he'll be back to bossing me around in no time. I'm not sure if this makes me happy or not.

"I am sorry about what I said before. I'm trying, but sometimes I can't stop myself," Sherlock said.

"I know Sherlock, it's just things have been confusing for me since you came back. Things are changing and I don't know what that means," I said and decided a change of subject was in order. "So I guess Donovan is still rubbing you the wrong way. After your death she would come in here going on and on about how she was right about you and that I was a fool for believing in you. I wanted to slap her."

"I don't think anything will ever change between the two of us. The look on her face when I walked back into the Yard was nice though." His words made me smile. I've always hated the way she treated him.

"I'm happy that you're home, even if it has made my life a little crazy," I stopped walking, looking up at him as I said this. I needed him to know that no matter what I was feeling right now I was glad he's here now.

"It's good to be back. I missed London, missed all of this."

We rounded the corner to the ambulance dock and I screamed at the scene before us. The two paramedics had been shot and the body they were transferring was missing. After I got over my initial shock I run to the one paramedic I have the possibility of saving knowing there was nothing I could do for the other.

"Sherlock, go get Lestrade and have him get someone down here from A&E down here to help me," I yelled. Instead of running back to the morgue he calls Lestrade while running over to me.

"What can I do to help?" He asked crouching down next to me.

"Keep pressure on his wound. I need to find some supplies in the ambulance."

It took me longer than expected to find what I needed, so by the time I jumped down from the ambulance we had a rush of doctors followed closely by Lestrade and Donovan. Thankfully that meant I didn't have to do much. I do much better with the dead than the living anyway. I am, however, not looking forward to the autopsy I'll be performing on the other paramedic later. I stepped back from the scene to get out of the way. Sherlock walked over to stand next to me, all the while taking in as much of the scene as possible.

"Are you okay?" he questioned, taking his eyes from the grisly scene before us to look at me.

"I think so. I just wasn't expecting any of this. Why would someone shoot two people just to steal a body? Why steal the body at all?"

"I'm not sure. There wasn't anything from the crime scene that would lead me to this conclusion," he said to me before turning to Lestrade saying, "Graham, I'm going to need copies of all of the photos from both crime scenes as soon as possible, and Molly is going to need all of the photos of the body from the first scene. I'll be in the pathology lab."

"It's Greg," Lestrade stated in a terse voice. Probably wishing that Sherlock would get his name correct at least once. "And I'll get them up there as soon as we're finished up here."

"You're going to work here tonight?" I asked.

"Yes, I was thinking that the two of us could work on this together. Your expertise will be very helpful to me."

"What about John?"

"John is out with Mary tonight and since I kind of interrupted his proposal when I came back I'm trying to be a bit more considerate. I'll text him."

"Okay, I guess we should head back up to the lab then. I'll need to call Tom and let him know I'll be extremely busy for the time being."

"You might want to clean up a bit too," Sherlock said as he motions to my hands and blouse.

"You too."

Looking over the pictures of the missing dead body, whose name was Joseph Alberston, I find nothing that Sherlock doesn't already know. After two hours of helping him sort through the photographs of the two scenes for clues they wheel in the paramedic who had been DOA. I wasn't really sure I was up for the post mortem, but knew it had to be done. I don't know what made his body any different from any other person I'd autopsied over the years, but somehow he was. Sherlock seemed to feel my apprehension and followed me over to the body.

"Why is he different?"

"Maybe because you stumbled on the scene and couldn't do anything to help him," the softness of his voice both comforted and concerned me.

He is never so caring. What is going on, what is so different now? Yes, I helped him, and we had a few romantic moments before he left. Despite those moments he was never really any different than his normal self. Now he was bringing questions to mind that I wasn't sure I wanted answered.

Whatever was plaguing me about the body dissipates with the confusion in my head, and I'm able to get through the autopsy without any problems. It was pretty straight forward, cause of death being a single gunshot wound to the head.

Sherlock had gone back to looking over the photos from the crime scenes, looking for whatever it was he must have missed. I watched him for a moment, the concentration on his face fascinating; the way he can see what no one else can has always captivated my senses. I shake my head before walking over to the sink to clean up. The heat of the water washed away some of the numbness that had taken over my body and brought out the exhaustion that I didn't know I'd been feeling.

"Sherlock, do you think it would be alright if we leave now? I feel like I'm about to fall over."

"Yes, of course. I can look at these darn things anywhere. I'll go get us a cab."

Sherlock tells the driver to head to my flat first even though Baker Street is closer. I doze off, my head resting against his arm. He doesn't seem to mind even though I know he doesn't really care for much affection of any kind. Once we've arrived at my flat he walks me to the door.

"You didn't have to walk me to the door Sherlock."

"I just wanted to make sure you're really okay. It's been a long stressful night. Is uh, Tom here to take care of you?"

"No, he said he'd stay at his place tonight since I wasn't sure how long I'd be. I'll be okay now that I'm home. I'm sorry I couldn't be more help tonight."

"I'll see you soon Molly," he said before heading back to the cab.

I let myself inside planning to just fall into bed. I don't care that I'm still dressed I just want the day to be done with. Instead I succumbed to the blackness before I get the chance to gasp.

I wake up not quite sure where I am. My mouth feels dry, like it's filled with cotton balls. The concrete floor is cold and hard making my body ache. I'm trying to take in all of my surroundings so that I might be able to figure out where I am, and hope that in doing so I'll be able to figure out how to possibly escape. All I can come up with is warehouse. It's mostly empty, a few scattered crates and of course this lovely floor I find myself on. I've never wished to be able to see things the way Sherlock does more than I do right now. He would know what to do, though he probably wouldn't have been ambushed in the first place.

"I see you're awake Molly Dear," the familiar sing-song voice makes me cringe.

"Jim," I said with a slight gasp. I shouldn't be surprised that he's still alive, but I am.

"Yes love, did you miss me?"

"No, not really."

"That's too bad, it would have made this much harder if I thought you had missed me. Of course that means now you'll be a nice toy to play with; to dangle in front of our favorite consulting detective. I underestimated you Molly. I didn't even look at you past the original access you gave me to Sherlock. The way he dismissed you whenever you were in a room showed just how little use you'd be to me. I never would have believed he would turn to you for help. Granted the fact that you would do anything for him probably helped in his decision."

"What do you want Jim?"

"I want what I've always wanted, to win the game. I do love playing games with Sherlock. It's always such fun to watch him gallivanting all over London trying to solve my puzzles. The more I can hurt him in the process the better. Since he thwarted my last game by living, thanks to you, we'll have to start a new game. This game shall have higher stakes. Did you know I once promised to burn the heart out of him? Now the question is how much do I want to hurt him and what will hurt him the most?" As he finishes he nods toward me.

"But I'm nobody, he was just taking advantage me like he always has. Using me won't hurt him, he doesn't care about me."

"Oh Molly, are you really that naïve? I know how Sherlock thinks, and you mean a whole lot more than you could ever imagine. It wasn't just that I wasn't looking at you or that you have a skill set that he could use to his advantage. He would have to trust you explicitly to ask for your help in faking his death," he said of this in that sing-song voice of his with a smile that makes me want to melt into the walls. "I've been keeping tabs on you my sweet Molly; had a good friend watching you. I know Sherlock stayed with you for weeks before leaving London. So tell me Molly, what really happened in those few weeks? Did all your dreams come true getting to play house with Sherlock Holmes? Then again maybe they didn't come true seeing as you seem to have moved on to someone else. Have you really moved on Molly Dear?"

"You've had someone watching me?" I asked, trembling for the first time since waking up in this damned warehouse. Did I say or do something that tipped someone off. Maybe I didn't look like I was grieving enough considering everyone knew I was in love with him. What am I going to tell Sherlock? Am I actually ever going to see him again?

"As soon as I discovered he wasn't dead and that is was you who helped make it all happen. It didn't take too long to figure out once he started taking apart my lovely criminal network. I've been waiting for him to turn back up in London so we could play again. I think it might be fun to send him a nice gift. In fact I'm sure you'll make a very nice gift for Sherlock. Yes, I think that will be perfect. Oh don't worry I'll let you live…for now."

"Why Jim? I don't understand," I managed between sobs.

"Because he's in love with you Molly Dear," is what I think I hear before blacking out.