Title: Doctor Molly (II)

Author: porpoise-song

Characters: Dr. Molly Hooper, The Doctor, Sherlock Holmes, Dr. John Watson, Captain Jack Harkness (well, hello there sailor!), then mentions of Lestrade, Donna Noble, Martha Jones, and Mickey Smith.

Rating: G (however, it may go up, by a bit though. Don't know...I haven't exactly planned everything out yet.)

Disclaimer: Unless I want Weeping Angels and the Crack to follow me (Steven Moffat), umbrella shaped bruises on me (Mark Gatiss), red coats storming my place (BBC), and a Victorian Age dressed zombie chasing me (Sir Author Conan Doyle) and some 60s/70s/80s dressed zombies (Doctor Who's respective owners, creators, producers, writers, actors, etc.), I need to say that I own absolutely nothing.

Summary: From anonymous: "After The Great Game, Molly runs into the Doctor (I was thinking Ten from when he thought he didn't deserve a Companion but which ever Doctor you think would suit is fine) She becomes his Companion for three years or so and after many adventures, he drops her off when and where he picked her up (and man that took long enough, didn't it?) But the next day, when Molly goes in to work, Sherlock knows there's something different about her. Her hair, her musculature, her confidence levels, the way she has to remember to react to talk about Jim or to him, something has definitely changed. Sherlock drives himself and everyone else nearly mad trying to figure out what happened to Molly. Then the Cybermen/Daleks/Archon attack St Bart's and only Molly knows what to do. bonus points for Martha Jones showing up to offer Molly a job with UNIT ala the "Want to see some more?" scene in A Study In Pink."

Warnings: Nothing really; spoilers for The Great Game, but, it's been over year since it's aired so I can talk about it. All. I. Want!

A/N: Prompt from anonymous at sherlockbbc_fic's Prompting XVI. Also, this in no way is in affiliation with my other Doctor Molly story. This said prompter said that she liked the original one, but said that she'd like a new one though (I didn't mind, of course). However, the Doctor and Molly probably met in the same way in the other story so - yeah. Also, of course, this is after the Ponds have left (not even going to mention how and when they left - they just left). The actual story is finished (if there ever was one, give me a shout please), but I've agreed (happily) to do one-shots of Molly either with the Doctor or afterwards. Either way - Molly is a total badass.

I hope you enjoy!


He had been brought in at the beginning of her shift. She had spent the last few hours trying to track down her boyfriend—or ex-boyfriend. She wasn't entirely sure if he not showing up at the Fox at six was his way of breaking up with her.

It doesn't matter; she thought to herself as the orderly quickly rushed out the door, Sherlock said he was gay and, although she wished he was wrong, her experience showed that he was always right. She let out a resigned melancholy sigh and unzipped the bag to reveal a man, in his late twenties that, at a glance, looked like he had died from some sort of poisoning. He isn't a bad looking guy, Molly thought studying him intently. His chin was a bit big and he didn't have distinct eyebrows—but, she let out another sigh, Sherlock wasn't attractive by normal standards either, but she was attracted to him.

She took a scalpel in her hand and made her way to his chest. "What's brown and sounds like a bell?" she muttered; her voice and smile strained with force cheerfulness. She always made little jokes and told stories to her cadavers. She patted the man's floppy brown hair before she lightly placed the blade on his chest.

"Dung!" the man suddenly yelled out.

"Ah!" Molly screamed out in terror, grabbing the metal tray and hitting it against his head.

"Ow!" he hissed out, grabbing his forehead and sitting up. "What was that for?"

"You're dead", Molly croaked out, taking a few steps back. "Dead people are supposed to stay dead."

"Well, that doesn't give you the excuse to give them a knock on the head."

"If anything, that'll teach them not to scare someone holding a sharp object", Molly snapped back, subconsciously taking a step towards him.

"I apologize for scaring you then." He looked around at his surroundings. "What am I doing in a morgue?"

"You were found in an alley near Trafalgar Square, dead by poison, it seems, and so, logically, you were brought to a morgue. However, the real question is how are you alive?" Molly took another step to him, somehow drawn to him.

"Is this what name they gave me?" he picked up the clipboard, ignoring her question. "Referral Number Eleven-Two-Eight-Eighty-Two?" He looked at her, accusingly, as if it was her fault that he was stuck with such a lousy name. "What rubbish."

"I was going to give you another name—a proper name", Molly said quietly.

"Like what?" he asked, his voice becoming excited.

Molly slightly blushed, thrilled to have a man—a good-looking man, at that—actually interested in what she thought. "A name like Pennyfeather,—nobody would ever forget a man with a name like Pennyfeather...and I would have given you an Oxford education as well. You would have been a happier man—wrestling with Plato in the morning, arguing with Voltaire in the afternoon, and having sup with Gibran in the evening. I would have made you a philosopher or an English professor, you see, and I think that could have made up for you dying, alone, in an alley."

"I have actually done those things", he muttered to himself, before he shifted himself off the gurney. "But, you would have given me all that?"

"Yes. It gets quite boring down here and an interesting case only pops in once in a while, as does he, and, so, I have to do something to amuse myself. Coming up with stories about the people in here does the trick—I don't know...I feel like I've given them a way to live one more time; living out their dreams and inspirations. Besides, you look like a philosopher...or an ancient traveller of some sorts."

He smiled warmly at her and his eyes were twinkling in delight and amusement, "Well, thank you Dr.—?"

"Hooper!" she squeaked out, blushing furiously. "Dr. Hooper, but you can just call me Molly."

"Well, Molly"—he started before he vociferated, "Blimey! I'm naked!"

Molly giggled and turned away, "Of course, you're naked! I was about to dissect you. Nevertheless, since you have an advantage over me and already know my name, you must tell me yours."

"The Doctor", he said, lazily grabbing the white sheet to cover himself.

"The Doctor?" Molly muttered out, before her face fell in realization. She turns back to him, "You're the Doctor! Of course you can't die! You change, but never die."

He smiled at her, "Yes, precisely. How did you know?"

"I'm bored most of the time and I have the internet", she glanced down at her scuffed, unisex shoes, "As you can see, I don't have much of a social life."

"Ah, well, I don't see anything wrong about that—having a social life is, simply, overrated." He leaned towards her, "By the way—you wouldn't happen to know where I could get some clothes, do you?"


He's messing with the TARDIS when she walks up to him, a suitcase in hand and her lab coat swung over her right arm. She's going to miss watching him fiddle around the TARDIS, acting as if he knows exactly what he's doing. He suddenly stops in his movements and turns around.

"You're leaving." He says it simply.

Molly lowly nods her head and glances down at her feet. "I don't want to—but, I have to. I got to." She looks at him and stares him in the eyes. "I'd rather leave by my own account—I don't want the decision to be made by another force." She's trying not to cry and go back on her decision.

He rubs his nose—trying not to cry, she thinks—and turns back around to grab something. "I want you to have these", he gives her a pair of black horn-rimmed glasses. "I want you to have my brainy-specs."

She takes them and studies them as he fondly remembers his encounter with his fifth regeneration. "Thank you Doctor", she says quietly and then looks back up at him; her eyes are glassy with tears. He pulls her into a tight hug. She digs her nose into the crook of his neck and deeply inhales, trying to stop herself from crying and to remember his smell. The smell will forever be burned into her brain and, if she tries, she'll be able to smell him when she's at her loneliest and at her end's meet: books, vanilla, and a hint of tobacco, although she's never seen him near the stuff.

"I should be thanking you too, Molly", he murmurs into her yellow wool coat. "Thank you for all the adventures and for saving my arse countless times."

She, with high regrets, pulls away and holds out her hand. "Goodbye Doctor. Visit me sometime—I hope to see you again." He shakes her hand and then nudges his head to the door. She picks up her suitcase and walks to the door. Her hand makes it as far as the doorknob before she looks back. "Do you remember when you told me that some of your companions are worse off after they leave?"

He slowly nods.

"I'm not. I'm a better person for having known you, Doctor; I'm a kinder, more confident, more independent woman 'cause of you. And I wouldn't trade anything in the universe for our time together—and I'm willing to bet that they wouldn't either." She smiles at him and he smiles back, tears shining in his eyes. Molly exits the TARDIS, hopefully not for the last time, and finds herself back in her morgue, everything the way it looked when she left three years ago (in relative time).

She steps away and watches the TARDIS disappear. Its wheezing sound is the most beautiful sound she's ever heard. She smiles and inhales a deep breath. She takes off her coat, places it and the suitcase under the table, puts on her lab coat, and goes back to work.


She enjoys wearing his "brainy-specs" while she's working. They make her feel smarter and more observant, although, if the Doctor were there right now, he'd be telling her that if she got any smarter; she'd be muscling in on his territory.

Sherlock and John enter her morgue about two hours after she returns, both covered in blood, soaking wet, laughing, and so pulveratricious. She narrows her eyes at them. "Lemme guess...explosion at a pool, judging by the scorch marks and the distinct smell of chlorine." She crocks an eyebrow at them, "Am I right?"

John sheepishly nods while Sherlock just frowns and quickly studies her. When she left, she had long hair that was tied up in a ponytail—now she has a neck-length, curly bob and, before, she was wearing some unflattering, unisex clothes, but she's now wearing a flattering gray dress that was showing more skin than Molly had ever shown at work. Lastly, and more importantly, she's wearing...makeup! Properly put on, right with her skin colour and face, eye, and lip shape, makeup!

"Molly"—John uneasily says. "Would you mind, y'know, patching us up?"

She glances at them and knows that arguing and her insistence that they go to Emerge would be futile. "Yes", she sighs out, "Why not?" She goes and gets the first aid kit, feeling Sherlock's intense and studying gaze on her the whole time.

Almost immediately, after she patches them up and sends them on their way, Lestrade comes in and asks her to come down to Scotland Yard for some questions about her boyfriend. There, they tell her that her "boyfriend" Jim isn't who she thinks he is. That he's really the criminal mastermind, Moriarty, who was responsible for all those bombings over the past few days, and that, only a few hours ago, tried to kill Sherlock and John.

She sits there, cool, calm, and slightly bored. She assumes that she's supposed to be crying (You're mistaken, Detective Inspector! she thinks) and blubbering, but she's not. And then, he gets to the part where he starts yelling at her and demanding that she tells him everything about Moriarty.

"I don't know anything about him", she says coolly. "Not at anytime during our brief and, if I say so, lukewarm relationship, did he reveal himself to be a criminal of any kind." She looks him in the eye. "He only used me to get close to Sherlock—I was just a pawn in his and Sherlock's game."

He lets her go shortly after, having nothing to hold her on. He believes her, but still has his doubts. Everybody does, honestly. She returns to work the next day, declining the hospital's offer of a two-week leave. "I'm over it", she tells them, rage threatening to burst into her soft voice. There must be some steel cord in her throat because, when another person tried to reason with her, she cuts them down like a file.


She hears about Moriarty when the Doctor takes her to London, 2021. She's closely following him as he explains the difference between Ju'wes and Re'nars, although they were nowhere near their planets. She suddenly stops when they pass a bookstore and stares at a window display for a book—written by Dr. John H. Watson about his adventures with Sherlock Holmes. By the time he finds her, she's one quarter of the way through it.

She's silently crying when he takes the book out of her hands. "Hey", he gently grabs her hand. "What's wrong?" She doesn't say anything; just flickers her eyes to the book. "Sherlock Holmes and Dr. John Watson", he picks up the book. "Very brilliant chaps, if I say so myself", he says casually.

Finally, out of frustration, she tells him everything. How she had a stupid, schoolgirl crush on Sherlock Holmes, how he used and toyed with her, and how incredibly stupid she now feels after reading about her would-if boyfriend, Jim, actually being Moriarty and just using her to get close to Sherlock.

When she's done spilling everything, he gently takes her hand. "You're not stupid—and it was not your fault. If Sherlock couldn't see it, then nobody could, honestly. Besides, if they can't see you for what your worth then—then the hell with them." He stands up, holds out his hand, and smiles down at her. "Now, I think a trip to the Eye of Orion will cheer you up quite nicely."


Sherlock and John don't appear back at the morgue for another week. "Trying to give me some space", she mutters to herself when she leaves for home. When she first arrives home after her long trip, she tracks down Toby and practically squeezes the life out of him. She curls up and falls asleep with him in her arms.

When Sherlock and John finally do appear back at the morgue, Sherlock is still giving her the same look he had after the pool explosion. She runs her hand through her hair, rubs her face, and cleans off her "brainy-specs", and, thinks to herself, 'Is there something on my face?' But, there's always nothing on her face, so, she continues in her work, a bit paranoid and self-conscious; however, before it can completely take over her and reduce her back to what she was before, the smell of the Doctor returns to her and she marches on, unfazed.

He really unnerves her—like pre-Doctor kind of nerves—when she casually says, with John and Lestrade in the room, that the fifty-seven year old, banker, Mr. Michael Anchovy, was poisoned by the prick of a needle by his son, clearly by the pattern of the bruises on his ankle. "Oh so sorry", she pushes her specs up and looks at Sherlock, "Were you about to say that?" Her smile slowly flattens when he gives her the look ('Times a million this time!' shethinks) and when she notices that both John and Lestrade are trying to suppress their laughs.

She leaves immediately and goes out of her way to avoid him for the next few days. She's quietly working in the morgue a week later when John slips in and silently and pointedly observes her taking Mrs. Winter's heart out. "Yes, John?" she asks softly.

"Hm?" John hums lightly, his eyes trailing up to her face.

"You're here to either pick something up or ask for something—either way, it involves Sherlock", she places her heart in a metal bowl.

"Yes, it involves Sherlock", John awkwardly rubs the back of his neck and avoids looking at her. "Sherlock—well...Sherlock has been acting a bit—strange and has been making everybody a bit—mad."

"John, I'd be more worried if Sherlock wasn't acting strange and making everybody mad."

"But—it involves you." Molly looks up at John through her specs. "He thinks that you're in league with Moriarty"—Molly heaves out an agitated sigh—"But, I told him that you're not with Moriarty."

"You're right", she says, turning her attentions back to Mrs. Winter. "I'm not nor would I ever be in league with That Man." She's trying to act as if it doesn't offend her, but, it overwhelms her, and she looks back at John, hurt on her face. "Why in the world would Sherlock think something monstrous like that?"

"I don't know", he rubs the back of his neck again. "This newfound confidence that you've found is a bit of a mystery to him—I just think that he finds it strange that you're acting like this. Well, frankly, we all do, but that's another story entirely. Lastly, he uses your new look as evidence—'clothes out of her price range', Sherlock says."

"This uncle of mine left me a load of money in his will." She shrugs dismissively, "I think that after all I've been through, I deserved a new wardrobe." She feels the need to make everything clear, and she continues, "And Sherlock's not all that and a bag of chips. I'm willing and ready to work with him, but only if he drops this nonsense."

John slowly nods, accepting her response. He leaves soon thereafter, the remaining time spent there filled with idle small talk and stony silence, and reports back to Sherlock. He's unsatisfied by her response and vows to figure it out.


He tells her everything—well, as much as he's willing to tell. She doesn't mind that—she's used to people not telling her everything; she's always had to figure it out on her own. The Doctor tells Molly about Gallifrey, the Great Time War, Daleks, and, most importantly,—because he spends the most time on it and stresses it the most—his past companions. Some leave not by their own choice, he says, and some are worse off by just being exposed to him.

He says it with such a resigned melancholy that she doesn't know how to react. She doesn't try to pretend that she understands what he's been through and what he's implying and, so, she gives him a sad smile and gently pats his hand. He seems content with that response and, immediately, he gives her a goofy smile and asks her where they should go next.

She's determined to make herself memorable. When she leaves, she wants to be remembered, like Sarah Jane or Rose. She never falls in love with him. She loves him like a brother, but she's never in love with him, which, frankly, comes as a surprise to both Mickey and Martha when they rejoin the team for an adventure or two.

She tells him that she loves him after a particularly emotionally draining adventure (that involved a woman named Donna Noble). There's fear in his eyes when he glances up at her, but it soon dissipates when he realizes that she loves him as a brother and his tired face softens.

She's brilliant, he says to Martha and Mickey before they leave, and she notices everything to a tee. They're usually mistaken for brother and sister because of this and, after the first dozen times, they just start accepting and introducing themselves as siblings.

"It cuts down on the confusion and, in some cases, the taboo", he tells her the first time he calls her his sister.

Molly is with him when the Master returns—with a face like Sherlock, she muses, but with ginger hair—and when the Master uses the Time Scoop to gather the last three Doctors. She's there when the universe is in danger and about to end—"again", the Doctor always kept quickly adding. She faces Weeping Angel, the Daleks, some Cybermen, and the Sontarans and she faces them with her head held up high, her mind clear and focus, and her hand in his.


Sherlock and John are running down the corridors of St. Bart's, away from an alien. The first time John's been near a real alien and Sherlock just has to screw it up by insulting its intelligence. Although the alien is short, ugly, and dumb, he's carrying a rather large gun, and that makes John rather afraid of it. "Basically a Yosemite Sam from outer space", John huffs out as they turn a corner, down another hallway, "And you had to make it angry."

At the end of this hallway, is Molly, wearing what appear to be golden yellow rain boots and her white lab coat. She's confidently standing there, with something behind her back when Sherlock and John pass her. John is about to grab her when she holds out her hand to stop him, steps forward, and then begins to speak to the alien.

"Pretty far away from Matriarchina, aren't you? About two hundred million light years away, I'd say." Cockiness is dripping from her words. He suddenly stops and lowers his gun, but he remains silent; still, she takes that as a yes and continues. "Matriarchina—isn't that a matriarchal planet?" She glances at Sherlock and John and smirks at them, not waiting for his response. "You see, the Matriarchina females are tall and beautiful while the males are short and ugly. And while the females are in charge of the government and run the society, the males are left to raise the young."

She looks back at the Matriarchinain. "Tired of being under the rule of Big Sister?" she says in a mocking tone and cocks her head at it.

It finally speaks; snarling in a harsh, deep voice, "I have no idea what you're trying to imply, but"—

"Oh! Short, ugly, and stupid." She stands up straighter and lets out a sigh to digress. "I'm invoking the Shadow Proclamation; Article fifty-seven, to be precise. This is a fully established level five planet—and you're going to invade it? What would your mother say to that?"

"I don't listen to proclamations nor do I listen to my maternal figure"—he growls out.

"Oh, c'mon—we all know that you lot are only invading Earth to prove to the rest of the universe that the males of Matriarchina are just as competent as the females." She then says to him in a low voice, "In addition, I think you may have a wee crush on your mother. But, don't worry—almost all male life forms in the universe have a varying degree of one."

Molly shifts her hands from behind her back and John notices that she has an umbrella behind her back. "We are a proud race and!"—

"Oh boy! Freud would be having a field day with this!" she giggles out, "But, that doesn't matter—all that does is this." She pauses and says to the Matriarchinain, in such a threatening voice, that John himself feels his toes curl, "Leave now and never come back—or else I'll have to kill you."

The Matriarchinain chuckles and an uneasy feeling begins to grow in John's stomach. "I do not accept threats from females."

"Hm, what a pity", Molly lets out a heavy sign and pulls out a remote from her coat pocket. "But, I warned you." She presses a button and the fire alarms start blaring. As she opens her umbrella, the sprinklers turn on, raining a yellow tinted liquid upon all of the Matriarchinains in the hospital.

The Matriarchinain starts to melt, like candle wax, and a lemony scent engulfs the hallways of the hospitals. Sherlock wrinkles his nose, "Lemonade?"

"Yupe", she says, cheerfully, holding out her hand from under the umbrella. "Being pumped down from the canteen. Lemonade contains citric acid, which, in high enough quantities, kills Matriarchinains." She turns to Sherlock and John, a grin on her face. "They have a low acidic tolerance."

"But—but, you killed it...him", John stammers out. He never expected Molly Hooper to kill anyone.

"I warned him", she stresses to him. "Besides, when he eventually and inevitably returned back to Matriarchina, they would have executed him anyways. But, they would have pumped him full of a diluted form of citric acid and, slowly, he would have burnt to death from the inside." She then shrugs, dismissively, "If anything, I saved him." She then bids them adieu and skips down the hall, humming "Singing in the Rain".


A week later, Sherlock and John walk into the morgue to find a brown-haired man in a trench coat lowly talking to Molly. Sherlock pointedly clears his throat and is greeted by a wide, pearly grin and a handshake. "Well, hello there—Captain Jack Harkness and who might you be?" he drawls out in a flirty American accent. "Oh", he notices John as well and looks him down, "and who might you be too?" He holds out his other hand out to John.

"Jack", Molly growls out and gives him a glare the Doctor would be proud of.

"Right", he tells her in a flat voice, looks, and points at her before leaving.

"Who was that?" John innocently asks her.

Sherlock lets out an exasperated sigh, not even going to bother to insult him with a sharp retort. Molly answers him though, with a kind response. "Captain Jack Harkness."

"What is he a captain of?" John asks her; Sherlock is acting like he doesn't want to know, although he does. From what he can deduce, he's knows that this Captain Jack is not really a captain, but introduces himself as one and is treated as such.

"Royal Air Force—retired though."

"False", Sherlock mutters so lowly that no one hears him. And, before John can continue with this tedious interrogation, Sherlock heaves out an annoyed sigh and John takes that as a cue to shut up. As she's giving Sherlock his metacarpals, her mind is buzzing with the conversation she was having with Captain Jack:

"You're a doctor—in fact; you're a doctor that has travelled with the Doctor for three years."

"Yes."

"Any good?"

"You wouldn't be here if I wasn't."

"Seen a lot of aliens then—unexplained events."

"Well, yes."

"A bit of trouble too, I bet."

"Of course—yes. Enough for a lifetime—far too much."

"Wanna see some more?"

"Oh god, yes."