So this just sort of happened a little while back, but I wanted to wait until I was finished with The Disappearance of Molly Hooper to post. When the first line popped into my head, I thought 'this could be a nice, lighthearted, fun sort of story!' But then a scene jumped into my head later that day and I went, 'Oh. Oh no.'

And this was born. I'm sorry. But it is bittersweet, not completely made of sad feels. Anyway, hope you guys enjoy it and that I've got John's voice down alright. Let me know what you think!

Disclaimer: I don't own Sherlock or Sherlock Holmes, I owe my thanks to ACD, and the BBC Sherlock team for such wonderful characters.

Everyone knew that John Watson made him a better man. Few realized that it was Molly Hooper who made him a good one.

It took me years to figure it out – decades, even – but when I think back to that difficult time in our lives, it's all very clear now. Sherlock Holmes had come back to us, miraculously alive. Three years. Three bloody years. Only Molly Hooper and Mycroft had known. Had been able to help.

I still don't know all the details of what transpired, and probably never will, but I understand the gist of it. It's not a time in my life I like to dwell on - thank God I had found Mary. And curse him to the depths of Hell for taking Molly away.

When he came back to me, to all of us, well…he was never the same, was he? No. But that was to be expected. No man goes through all of that and comes back unscathed. I think her death affected him most of all, though.

It was right before Sherlock made his reappearance into the land of the living. According to the official police statement, Molly had been the victim of a petty thief who was after the contents of her purse. Turned out the bloody idiot had been in possession of a gun. We were all outraged. It just wasn't fair for a good hearted person like her to suffer such a useless death at the hands of a selfish one. Greg always got particularly upset when it was brought up; I always assumed it was because in some way he felt a general responsibility as an officer of the law.

She was there for all of us, you know. Always. She saw the worst of me but she was stubborn. Surprised us all a bit, too, I think. I don't know what happened between them when he was gone. I know only that he stayed with her when he had nowhere else to go, or couldn't fix his wounds on his own.

I still remember quite vividly the first time he returned to St Bart's after…everything. It was almost two months after her passing.

"Sherlock, you're going to wear the floorboards out with your pacing, and what will Mrs. Hudson say then?"

As usual, John was ignored and Sherlock continued to mutter to himself agitatedly. As he turned into the kitchen with the intention of putting the kettle on, John managed to make out an, "I don't care what Mycroft thinks" and then a, "And what exactly is that supposed to mean?"

Minutes later, just as the kettle was starting its high pitched whistle indicating that John's overdue cup of tea for the morning was nearly done, Sherlock popped in the kitchen, enthusiastically buttoning his trademark coat. "We're going to Barts," he declared. With a sigh, John turned off the stove and threw the nearest jumper over his head.

His fiancée, Mary, had been the absolute best. While John had moved out of 221B and he and Mary had been only weeks away from their wedding, it was clear that Sherlock needed John's company more than ever upon his return. Mary had understood and they agreed to push the wedding back a year where John would return to 221B until then.

Everything was normal as we exited the cab and strode through the front doors. Sherlock had appeared singularly focused; he had taken a case Lestrade really needed an extra pair of eyes (his eyes) on. It wasn't until we began reacquainting ourselves with the lab in the morgue that everything went to shit.

John looked around and felt a growing pressure in his chest. Something – someone – was missing, and the place just felt cold and wrong. He glanced at Sherlock, wondering if his often times detached friend felt it as well.

Sherlock strode to the table where he had spent many an hour looking through his microscope. He was being far too quiet.

"Sherlock?"

Sherlock then made his way to the cabinets and rifled through the contents. His eyes narrowed. He walked briskly over to the office. Molly's office. Or had been. He was inside for a minute. Two minutes.

"Sherlock?" John inched his way over to the office. "It's ok. Sherlock talk to me." John began to worry when his eyes found the consulting detective once more. He could almost see the tension building up in the tall detective like a great cloud of sparks about to catch and implode.

The catalyst was the sound of the doors to the morgue opening and closing, and an unfamiliar face striding inside to stare at them.

Boom.

"DAMNIT, JOHN, IT'S NOT OK! Have you seen this place?" Sherlock seethed, gesturing wildly around them. "It's wrong! Everything is wrong. Wrong, wrong, wrong, wrong, wrong!" He was growling now and viciously making his way over to the poor sod that had just come in. The stout man cowered and tried to respond.

"I-I-I'm so-sorry?"

"What have you done to this place?" He roared at the man as he ranted on. "You've ruined the filing system, the equipment is not properly ordered and where it should be, my microscope is gone, and where is the pink coffee mug in the office? You imbecile. You absolute, god forsaken useless human being."

John had been literally stunned up until this point. Finally his brain snapped into action as Sherlock momentarily turned his back on the terrified little man with a frustrated tensing of muscles. Not knowing what Sherlock was going to do next, John rushed the terrified man back to the morgue doors and apologized as he shoved him out. The situation would be explained to him at some point, no doubt. John then closed and locked the door. This scene wasn't meant for anyone's eyes, but John couldn't leave the grieving man alone in good conscience.

Sherlock hadn't really said much at all about Molly since her death, and I don't believe he really knew how to deal with the emotions of it at the time. It took two months – Two months? Oh, Sherlock. – for all of the turmoil to come rushing out in the most terrifying bout of rage I've ever seen. And I was an army doctor.

John watched in a horrified sort of fascination as the aloof, "emotions are predictable, boring" Sherlock Holmes unleashed his fury upon the unsuspecting morgue. Expensive equipment was slammed against walls, glass shattered and drew blood, fists pounded mercilessly against locked container units. At one point he had started shouting "No! It's not right!" as if alternately retorting and pleading with someone.

The worst were the tears running down the consulting detective's cheeks. John had only ever seen Sherlock cry once before, but that had been part of an act. He looked on, feeling at the same time an intruder and helpless bystander as his friend began to lose steam.

It ended up being the oddest, yet most appropriate thing that actually caused the last of his anger to ebb away.

Sherlock had made his way into her old office again, breathing deeply in and out, eyes wild. However he made no move to strike, as if destroying anything in there would be destroying Molly. When he did emerge a little while later, he had something black and thin in his hands.

A riding crop.

Somehow they had missed the riding crop stashed in one of the lower corner cupboards when cleaning her office out. It was the one she kept on hand because she knew he liked to run experiments with it now and then. The one she had held on to because she knew he would be back for it.

Sherlock heaved a shaky breath, staring at the object reverently held in his hands. After a moment he laughed quietly, as if privy to a private joke. Only then did he look up, eyes connecting with John's. Still clutching the riding crop tightly, he glanced around at the damaged lab.

He straightened himself up (as much as he could), strode over to John and uttered a hoarse, "I'm sorry." It was unclear whether he was apologizing about the destruction or out of embarrassment over him being witness to the outburst. John simply did the only thing he could think to do. He shrugged kindly and patted his friend's hunched, drained form (a disturbing look on the normally energetic and confident to a fault consulting detective) and kept a steady arm around him as he led them out of the morgue and back to Baker Street where they could have their privacy.

As they had waited for a cab John pulled out his phone and began typing out a text. Before he could even finish his phone pinged and he read the message.

Already on it. The footage has been erased and my men are on there way to replace all damaged equipment and deal with Mr. Yabez. No one will be the wiser, my brother need not worry. - MH

John released a heavy sigh. For all their bickering, the Holmes brothers did care for each other when it counted.

Thanks. – JW

I have never once accused Sherlock of being heartless or emotionless since that day. It was the most human thing I've ever seen him do, and apart from his fake suicide, the most painful thing I've ever had to watch. After that, little by little, he began to change.

It took years, mind you, but he started to be more polite to clients, more considerate and agreeable to those of us lucky enough to be called his friend. He would surprise me more often by taking cases that seemed to me to be below a 6 or 7, with the excuse that he may as well solve a problem if he had nothing better to do. As his manners improved he also became decidedly more gentle with the quieter or more flustered clients – especially women.

I admit that sometimes I was guilty of trying to persuade him to the possibility of a relationship with a few of the more interesting and sensible women we met on cases, but he would have none of it. There would be an emphatic, "not interested John", followed by a period of melancholy silence for the rest of the evening.

Over the years he began to…mellow…for lack of a better word. That's not to say that he lost his quirks, though. Oh no. Sherlock still retains his endless curiosity for running mad experiments and that spark for a most intriguing case to be solved. He still grins a bit too much when there is a triple homicide and Lestrade grudgingly asks for his help.

One day upon a regular visit to 221B Baker Street he was, I suppose, bored enough to explain it to me. Or perhaps he simply wanted someone to know.

"It's Molly, John."

Startled, John looked over at his mate with the same astonished look he had given him upon the first time they had met all those years ago.

"You're thinking out loud again." Sherlock explained with a wave of his hand. "I've explained my methods and reasoning countless times to you, but you have yet to seem unimpressed with my conclusions. Curious."

It was true, these days John Watson mostly understood how Sherlock often arrived at his answers, but he didn't think he would ever cease to be amazed by the man. He shrugged in response. He had been pondering Sherlock's development as a person since he had met him, and specifically attempting to peg what it was that had been the catalyst into making Sherlock the man he was today.

"Molly? Molly Hooper?"

"Of course." The kettle sounded and Sherlock waited until John returned with two steaming cups and had settled comfortably back into his chair to continue. "She never left."

A bit concerned, John eyed Sherlock. There was no way that Sherlock Holmes could believe in ghosts…could he?

Sherlock swallowed some tea and rolled his eyes at John's furrowed brow. "Don't be ridiculous, John, of course not."

Not following, John uttered his confusion. "But then how…?"

Sherlock smiled slightly and pointed to his head. "My mind palace. Molly has been growing old with us my dear friend. Do you remember after the Fall, after I returned?"

"How could I forget?" John was leaning forward now, eager to learn more about how Molly Hooper had been improving Sherlock all this time.

"The night we buried her ashes I spoke with her until morning. All the information I'd gathered and stored on her over the years – continue to gather – pulled together to form an embodiment of her in my mind palace. We roamed the halls and rooms together for hours that night, talking about bacteria cultures produced by saliva, of all things."

At this John had to laugh. It was so…them. "You would." Sherlock, too, grinned at this.

"The day of the memorial I retreated to my mind palace to just sit with her in her room. I'm not sure either of us actually said anything, but she didn't let go of my hand until we returned home." Sherlock shook his head, as if he still found that particular action to be sentimental folly, but endearing sentimental folly.

"That day we returned to the morgue," here Sherlock took in a breath as if the memory was sharp, to be handled carefully. "I wouldn't listen to her. Molly was insisting that I wasn't ready, that Mycroft knew this and was looking out for me. I was angry, I didn't want to be weak any longer."

John nodded, a silent encouragement to continue.

"When I…snapped, well she tried to stop me. Her words weren't harsh – could they ever truly be? She continued to repeat that it was alright, and, essentially, that I was being stupid because of course things would be different. I would hear none of it. Not until I found the riding crop." He glanced toward his room where John knew the riding crop to be locked safely in the drawer by his bed.

"After that Molly continued to assert her presence, even when I wasn't fully in my mind palace. I would hear her voice reprimand me for snapping at a client or disregarding you or Greg. I imagined her reaction to my apathetic dismissal of that abysmally boring case involving the six year old girl and a cat named 'Fluffy'. She would refuse to speak to me in my mind palace for days if I was callous toward another's life. God, I even began seeking her advice in buying the obligatory gifts at Christmas or couldn't decide what to wear!" Sherlock made a familiar motion, agitatedly running his hands through his dark locks.

"Wow. Guess I should thank Molly for the sensible gifts over the years then." They both chuckled and continued to chat about Molly Hooper until John bid him goodbye. When he returned home, John admitted his surprise at the small pathologist being such a large influence on their stubborn friend to Mary. His wife simply smiled at him serenely and said she was glad.

I asked him once if Molly appeared older or the same age he'd last seen her in his mind palace. He said that from the images of her parents coupled with Molly's own maturation from pictures he'd seen of her as a child, he was able to map out an accurate image of her at any point in life. In his mind palace, she aged as they aged.

Though he had admitted once that he'd entered his mind palace and projected a younger her, as she'd been when they first met. Apparently a bloke could be slapped in his own mind palace.

The years have continued to go by, and some things have changed while others remain far too similar. Mrs. Hudson passed away and her niece, who is uncannily similar to her, has taken up residence as the 221 Baker Street landlady. Lestrade never managed to move on from his ruined marriage, but is content with his life and having children who love him. He swings round to play weekly chess matches with Sherlock these days (he has yet to last more than 5 minutes, but it's a better excuse than 'drugs bust' to share a drink and discuss the most recent criminal scandal on London's streets).

Mycroft has retired, but still carries around an umbrella and keeps a close eye on his little brother and his "associates". I suspect he still has a small team, lead by Anthea, at his beck and call. Sherlock and he continue to throw petty insults about diets and real jobs at each other.

Yes, some things never do change.

"Feeling sentimental?"

I glance up from my laptop to see the door to the house ajar and an all too welcome face peering at me, knowing far too much from a single glance.

"Oh, yes, I suppose. Tea?" He nods and finds his way to our usual spots when he decides to visit our place for a change. I fix the tea how each of us likes it and join him in the chairs by the sitting room window.

"Mary's out shopping with the grandkids today. Said I wasn't allowed to come, something about me being a right spoilsport." I grin as I think of my wife and family. Of course, Sherlock already knows she's out – probably planned to come today because of it.

We're silent for a while, sipping our tea and simply enjoying the quiet companionship. When Sherlock breaks the silence, it's with a serious focus that I haven't seen grace his features for some time.

"John, there's something you need to hear." He seems hesitant, which has never been a good look on him.

"Ok." I say.

"It's about Molly Hooper. How she died." I immediately sober, and give him a questioning look.

"Why bring it up now, after all this time?"

He pauses, searching for the right words. Maybe Molly is the one dictating them. "I made a promise that I would keep her death a secret. You know, I died and she kept my secret until the very end. And here I am, alive, too selfish to do the same." His face gives the slightest indication of the shame his words hint at.

"Sherlock…what are you talking about?" I'm growing uneasy, neither of us are fond of bringing up the events surrounding the Fall.

"I think you deserve to know the truth, though, John. We're old now, and what's done is done. I believe you're ready to know." A slight eye roll on his part leads me to believe that Molly is protesting all of this to him in his mind. "And I believe that her words deserve to be heard."

I was taken back to a familiar time, long ago, but an unfamiliar scene.

It's a chess game, and these are the final moves. Sherlock was standing at one end of Molly's sitting room, a tall man with a predatory grin and a gun at the other.

"Your boss is dead Moran, your network is gone. There would be little point."

"Ah, you don't understand Mr. Holmes. I owe you a death, and I have one move remaining in the game."

"I refuse to play."

Moran made a tutting noise and shook his head as if dealing with a child. "I had heard you were a smart man, Mr. Holmes. But you don't seem to be grasping the rules of the game completely." Left hand pointing a gun at Sherlock, his right hand reached into his pocket and pulled out a phone. "You give me your answer, I send a text with the name you give and the game is done. If you stay silent, I press this little button here and choose for you. Off goes the signal to send Mr. Watson to his grave."

Sherlock made an impatient, frustrated noise at the back of his throat and furiously ran his hands back and forth through his hair. His brain was processing and pulling up data, trying to find a solution in the little time he had.

As he struggled through scenario after scenario, the smallest of movements caught his eye, though Sherlock made no outward sign of noticing anything but the man in front of him.

Another piece in the match.

Molly Hooper stared at the scene before her. She was supposed to be at work right now, but an unexpected reaction from Toby had her making arrangements to go to the vet instead. Further unexpected events had her silently peeking out from the doorway to her bedroom at the standoff in her sitting room. The dangerous looking man had made an appearance in her flat followed immediately by Sherlock Holmes just minutes before.

She knew Sherlock was watching her, however discreetly. He was facing her while Moran's back was to her. So, as carefully as she could she touched her pocket where the shape of her phone could be seen sticking out.

Sherlock understood. She had phoned Lestrade. He clenched a fist tightly. Go back in your room, wait.

Molly retreated slightly, back against the wall next to the doorframe and breathed in shallow breaths. She started as the unfamiliar voice shouted from the room beyond. "I won't wait much longer Mr. Holmes. You have one minute or your silence makes the decision for you! Lestrade? Hudson? Watson?"

She had a choice to make now. She released the latch on the carrying case a few feet away and pet the cat that made to dart out with a steady hand. It was then that she noticed the shoes she had been about to put on. Standing once more, she straightened her back and sucked in a steady breath to reinforce her resolve.

Sherlock was stalling for time with pointless words when she reappeared in the open doorway. When he saw her he raised his eyebrows.

Don't you dare.

A shoe flew across the room and landed its mark on the assassin's arm. Everything seemed to move in slow motion from that point. With obvious surprise the phone was released from Moran's grip.

As soon as the shoe had left her hand Molly had started to charge the man with the gun. Sherlock scrambled to collect the fallen phone that had slid closer to him. His hand closed around it and he was making a forward movement to attack Moran when a shot rang out.

His knee knocked the gun from Moran's grasp seconds later and his fist collided with the man's snarling face. Molly fell to the ground. Sherlock's fists continued to find purchase anywhere they could on Moran's body before one hand found the gun and whirled it on Moran.

They need him alive. They needed him alive for Sherlock to redeem himself. Molly was feebly attempting to remind him of that. He swung the gun at Moran's head and the man fell limp beneath the detective.

Heavy breathing. Dialing. "I need an ambulance." A discarded phone.

Sherlock kicked at Moran's unconscious body and crawled over to where Molly lay gasping for breath. One glance at the blood pouring out of her stomach and he knew the wound was fatal. The ambulance didn't have a chance. She knew, too. "Why? Why did you do that…stupid!" He was angry. "Why didn't you just stay hidden?"

"And let you or John die?" Molly gasped out.

"I would have figured something out Molly!"

Instead she grimaced at him in an attempt to smile. "It's ok. I-I-I'm not afraid to die for you, Sherlock. You," she coughed and red stained her lips, "you helped me, even if you never understand how. You help other people, too. M-more than I ever could. If my death saves you Sherlock, then I'm very glad."

Sherlock simply sat there and for once in his life was at a complete loss for words. All he could mutter was a continuing stream of "stupid, stupid."

She grabbed his hand and held it tightly. "Li-li-listen to me, Sherlock," she gasped. "If you had let Greg or Mrs. Hudson die, you would never forgive yourself. If John died, you would be broke-broken. I saw the options," her breaths became shallower with each word, "and I made a choice. If I died, you could still become a good man. And th-this was my-MY choice. Please, no - Don't you da-dare forget that. And don't you dare tell John. You have to promise me, Sherlock. You have to keep this secret. I don't want him to suffer any more than he already has." Her eyes pleaded so fiercely with his own that he could do nothing else but nod his agreement. He wouldn't tell.

She was appeased by his response and her eyelids began to droop, as if she could go now. Her lips moved slowly with the effort of speaking again. "I know you don't think love is very admirable, but I-I love you, Sherlock Holmes."

At some point Sherlock realized that Toby was moaning low and painfully next him. Molly made one last attempt to smile at him. They sat there together for what seemed like hours, Molly breathing in painfully and her grasp on his hand loosening by the second while his hold on her tightened.

In reality it only took minutes for the life of Molly Hooper to slip quietly away in her flat.

Greg burst into the flat, took in the horrific scene in front of him, and immediately made his way over to Molly. He glanced at the pale man holding onto her painfully and didn't recognize him at first. A double take had him staring into a pair of unseeing eyes that were vaguely familiar. "My God." It couldn't be, could it? "Sherlock…Is that you?" Three years and a war had changed him.

Greg was made to swear to write a false report of her death and keep the truth hidden. Mycroft arrived with word that the final hitmen had been apprehended, and was only able to take Molly's body away with repeated assurances to Sherlock that she would be treated with the utmost respect, and that he could visit her the following day.

The next morning Sherlock had reappeared at 221B Baker Street for the first time in over three years, a cat in hand.

That night Mary Watson accompanied her husband to the garden where the petit pathologist's remains rested. She sent a silent prayer of thanks to the woman she had called a good friend, then stepped back to give her husband time to do the same. She watched as he gently laid four sunflowers on her grave and began to speak.

"I know you loved sunflowers, Molly. You worked in a morgue but you liked the way they were bright and full of life. They remind me a lot of you."

"There. One for each of us that you saved. Mary insisted on bringing her own – I think you're probably grinning at the purple nightshade - she certainly was." He was silent for a moment before continuing.

"Thank you. You succeeded, you know. He's not just a great man anymore, he's a good man." He started to rise, and Mary assumed he was ready, but he hesitated a moment as if deciding he should press on and just say it.

"He loves you, too. I know, you're blushing and telling me that's not right, he just appreciates what you've done for him. But honestly, it's not hard to tell – you live in his mind palace, by the way, did you know that? I think it took him forever to figure it out, though. Hell, he's still too stubborn to call it that. There was one time a few years ago... he started asking me if I regretted any of my choices up to this point in our lives. Eventually he got on about if he had ever dreamed of settling down…well, he didn't complete the thought but instead smiled sadly and continued to sip on his coffee – still black, two sugars – from a pink mug covered in cats. He still keeps everything that reminds him of you, that keeps you alive for him. Yeah. I'm pretty sure he raided your flat the night before your brother came to claim your stuff, actually." John continued to gaze unseeingly for a minute, caught up in some memory.

"But look at me, I'm an old man rambling now. Molly Hooper, thank you for saving my life, twice. Thank you for being the bravest and most selfless woman I know. And most of all, thank you for believing in him."