The Doctor eventually found Molly's appartment building. It was a few hours after the scene in the lab, and he hoped she'd gotten over enough of her embarrassment that his appearance wouldn't just fluster her further.
As he walked down the street towards the building, he noticed a familiar form standing outside, seemingly waiting for something. Molly.Right, her boyfriend had said something about picking her up around five.
Warning bells went off in his head when a cab pulled out in front of her and an unfamiliar form emerged and talked to her. Molly froze, and after a few moments, she followed the man into the cab. The Doctor had already quickened his pace, suspicions aroused, but he didn't break into a run until he saw the figures struggling inside the cab. "Molly!"
He got close enough to see Molly's terrified face from within the car, then the cab took off, picking up speed faster than the Doctor could hope to. "No!" He raced after the cab as fast as he could, but he couldn't hope to out race a car, even in London traffic. It drove off out of sight, and he was left panting, trying to gather his thoughts.
He wasn't sure why Molly had been taken, but he could take a guess at who the real target might be. It was either himself, as per usual, or the mysterious Sherlock Holmes. He was brilliant, so he was bound to have made some enemies, and he seemed to be tangled in some governmental affairs judging by the text from his brother.
The Doctor ran up to a young man on the street listening to music on his smart phone. "Excuse me, can I borrow that for a moment?" After shooting him a suspicious look, the man oblidged, hovering nearby to make sure he didn't run off with his phone.
He had no time for subtlety, so he simply pulled out his sonic screwdriver and gave the phone a bit of a zap. He scrolled at super-speed through the results for Sherlock Holmes, quickly discovering his website, "The Science of Deduction." The skill he uses is induction, not deduction, he thought irritably for a moment, but that thought was chased from his head when he saw Sherlock's latest post. "Found. The Bruce-Partington plans. Please collect. The Pool. Midnight."
After a bit of quick research, he was able to figure out that the pool referred to was the pool where Carl Powers had died. He found the address, passed the bewildered teenager back his now-enhanced phone, and took off to hail a cab.
The Oncoming Storm was beginning to brew under the surface. Far too many people were going after his companion, and they needed to learn that his companions were off-limits.
SCENEBREAK
Molly groaned slightly as she came back to consciousness. She still felt a little light-headed and dizzy, but the feeling started to pass the longer she was awake.
She opened her eyes to see that she was in some sort of changing stall. The air had the strange humidness that was unique to pools, which would fit with the damp floor of the stall she was in.
There was some sort of device in her ear. She went to remove it, but her groan must have been heard, because a familiar voice sounded in her ear. "Ah, look who finally woke up."
She froze. "J... Jim?" Her still disoriented mind didn't understand. Why had she been kidnapped, and why was her boyfriend speaking to her through an earpiece? She shook her head, trying to clear it.
"Hello dear," he said in a too-smooth purr, "Did you enjoy that little show in the lab? You played your part quite well. Not that you knew what you were doing, of course. How could you? Bumbling, clueless Molly Hooper." The words were harsh, cutting into Molly's mind, right into her greatest fears. "The girl with the crush on the great detective." He chuckled cruely. "Well, you've set your sights rather high, haven't you? Why would Sherlock Holmes ever look at you? What do you think he could possibly see? What could anyone?"
Molly drew in a sharp breath, trying to hold back the tears as her boyfriend threw all of her darkest fears in her face. "Stop it," she whispered.
"Did you really think he'd ever look twice at you? You? Seriously? You were there to be used."
"Stop it, I said stop it!" she cried out desperately.
A high-pitched laugh sounded sharply in her ear. "Sorry there girly, but I'm the one giving the orders. Or haven't you noticed what you're wearing?"
The pathologist froze in horror. She had been too disoriented earlier to realize that she was wearing a large jacket that wasn't hers. Hands trembling, she drew back the flaps of the jacket, revealing a bomb best. She let out a choked cry at the sight, but she didn't scream or cry. Neither would do her any good. Her head was beginning to clear, and she knew that she would have to stay calm and logical if she was going to get out of this alive. In a low, even tone, she asked, "What do you want?"
"Ah, now you get the picture." His voice became dangerously low as he told her, "You're going to do everything I say. Got it?"
Gritting her teeth, she gave a short, "Yes."
"Good girl. Now do shut up. I don't need you getting all snively. Let's save that for our special guest, shall we?"
Molly shut her mouth obediently, mind racing. Clearly, this was a trap of some sort, and she was the bait. But who would come for her?
She could only wait in silence.
SCENEBREAK
She didn't have to wait long. Only a few minutes had passed when she heard nearby doors being opened. The normally quiet footsteps echoed loudly in the empty building. "Brought you a little getting-to-know you present." Molly started at the familiar voice. Sherlock!
The detective continued calling out to the person he seemed sure was there. "That's what it's all been for, hasn't it? All your little puzzles, making me dance, all to distract me from this."
Molly wondered briefly if she was supposed to respond. She was saved from having to decide by the sound of another door opening - it sounded like it was from a stall near the one she was in. A familiar, deliberately level tone greeted Sherlock with a short, "Evening."
Her eyes widened. John. Sherlock repeated her thought in a low, horrified tone. "John. what the hell?" Molly was truly confused now. Was John working with Jim?
"This is turn-up, isn't it Sherlock? Bet you never saw this coming," John taunted dully. Molly listened more carefully to his tone and realized he was parroting someone's words. He must have one of those earpieces in, and Jim was feeding him his lines. The question was, why? What was it all for?
John's next words confirmed her theory. "What would you like me to have him say next?" After a few moments, he began parroting dully, "Gottle o' gear, gottle o' gear, gottle o' gear."
"Stop it," Sherlock ordered in a low whisper.
"No?" John questioned. "Then maybe you'll like it better from a prettier mouth than mine?"
Jim's voice sounded in her ear. "Go outside the door and stand next to John, then repeat what I tell you."
Trying to ignore the way her heart was trying to beat its way out of her chest, she got to her feet and pushed past the door. John and Sherlock were standing out beside the pool; Molly did as Jim had said and came to stand beside John. He too was wearing a bomb vest, and little red laser dots danced across them, speaking of a gunmen off in the shadows aiming at him. Sherlock looked at her in surprise and worry for a moment, but quickly returned his horrified gaze to John.
Listening to Jim's words, she repeated as calmly as she could manage, "This one's a pretty catch, isn't she Sherlock? But far too easy to fool." She closed her eyes as he forced her to repeat his vile words. "Not worth much to you, I'm told. But she makes for pretty bait all the same. Stupid little Molly Hooper, desperate enough to grab onto the first man who came her way."
"Nice touch this," John took over. "The pool, where little Carl died. I stopped him..." the former soldier trailed off, taking a moment to collect himself before continuing, "I can stop John Watson too, stop his heart. I'd let Molly live for you to kick around some more... but where would the fun be in that?"
Sherlock was looking more worked up than she'd ever seen him before. Staring wildly around the shadows of the pool, he called out angrily, "Who are you?"
Somewhere off in the shadows, another door opened, swinging closed with a slow, eerie screech. "I gave you my number," Jim's voice called out mockingly, every syllable twisted and exaggerated. "I thought you might call."
Her boyfriend stepped out of the shadows, but it wasn't the Jim she'd known. Instead of the t-shirt and sweats he normally had on, he was wearing a suit and tie, with his normally docile face whirled into a cruel smirk. Everything about him was different, every line seemed sharper. But his eyes were the worst. His warm brown eyes now seemed almost black, and they were completely cold and empty. She'd never seen eyes so cruel before.
The strange man began advancing towards them, hands in his pockets, smirk focused on Sherlock. "Is that an Army Browning L9A1 in your pocket," he quipped, "Or are you just pleased to see me?"
Gaze focused intensely on Jim, Sherlock slowly pulled a gun out of his pocket, pointing it at him. "Both."
Jim halted, bouncing ever so slightly on the balls of his feet. "Jim Moriarty," he introduced himself. "Hi-i!" Even his voice was wildly different. Instead of the meek, soft accent from before, his accent oscillated wildly, occasionally slipping into an eerie sing-song. Everything about it just sounded wrong.
When Sherlock didn't respond, his tone grew mocking. "'Jim? Jim from the hospital?'" Still nothing. "Huh. Did I really make so fleeting an impression? Although I suppose, that was rather the point."
When Sherlock continued to point the gun at him, Jim - no, Moriarty - just scoffed. "Don't be silly, someone else is holding the riffle. I don't like getting my hands dirty." He grinned cruelly. "I've given you a glimpse, Sherlock, just a teeny glimpse, of what I've got going on out there in the big bad world. I'm a specialist, you see. Like you."
Sherlock didn't move an inch, but his expression shifted slightly into one of understanding. "'Dear Jim,'" he breathed, gaze fixed on Moriarty, "'Please will you fix it for me, to get rid of my lover's nasty sister?' 'Dear Jim, please will you fix it for me, to disappear to South America?'"
Moriarty chuckled, looking impressed with Sherlock's shrewdness. "Just so."
"Consulting criminal," the consulting detective mused, looking almost impressed with the monster in front of him. "Brilliant."
"Isn't it?" Moriarty gushed. "No one ever gets to me." His voice grew dangerously still as he added, "And no one ever will." His gaze slid past Sherlock, staring into the shadows by the door. "So if you're trying to be sneaky, Doctor, you can just give it up now. Come out and play with the big boys."
Molly tensed in surprise as the Doctor stepped out into the light. She took an involuntary step towards him, starting to call out to him, but the feeling of the semtext vest against her chest silenced her again. The Doctor's gaze flicked quickly to her, eyes widening in horror when he saw the bomb strapped to her. Then his expression grew curiously blank – dangerously blank. She had learned well that the Doctor was at his most dangerous and angry when he seemed totally emotionless.
"Thought it was worth a shot," he explained lightly.
Moriarty's smirk grew even wider. "The great Doctor himself. Well well, this is an honor, isn't it?" Amused sarcasm radiated from his tone. "The last living Time Lord."
The Doctor's gaze narrowed, but other than that he didn't react. "On my better days. That's not exactly common knowledge, though."
The consulting criminal just chuckled. "UNIT has some pretty extensive files on you, Doctor. It's child's play hacking in. I mean really, one password for everything? It's like they're not even trying." His evaluating gaze slid over the Doctor, looking him up and down. "Well, I have to say, when I met an alien from outer space, I expected him to look a bit more... impressive."
The Doctor just stared quietly back at him, but Sherlock's brow furrowed slightly in confusion. "And here I was thinking you were perfectly sane," he commented lightly.
Moriarty's sharp gaze flicked between the Doctor and Sherlock. "Oh, don't tell me you don't know." When Sherlock continued to look surprised, he laughed delightedly. "Really? Brother dearest didn't see fit to tell you? Aliens are real, Sherly old boy, and this one here's the biggest and baddest of them all. The last living Time Lord, because he killed all the others. Destroyed his entire species." His tone had turned sharp, his words cutting. "Now he bangs around in his little spaceship, traveling through time and space, trying to save the world while the people around him get killed."
Sherlock rolled his eyes. "Time travel is impossible," he informed Moriarty. "The paradoxes and minor changes would ripple into too many effects."
Moriarty smirked mockingly. "Oh come on, Sherlock. Being a genius doesn't mean you can't keep an open mind."
Molly had tuned out of their conversation a while ago. Moriarty's words had stunned her into shocked silence. The last living Time Lord, because he killed all the others. Was it true? Could it possibly be true? Had the Doctor really destroyed an entire species – his own? She remembered his earlier reaction to genocide, how horrified, how familiar he had seemed with it.
The Doctor's voice broke her out of her thoughts. "If you've read so much about me, then you know what happens to people who hurt my companions." His calm tone barely covered the rage underneath. He was really, truly angry, Molly realized. Because of her.
Moriarty didn't seem bothered by his tone. Instead, his cruel smirk turned into one of amusement as he turned to look at Molly. "Yes, Molly Hooper, companion of the Doctor. I wasn't going to come after you, Doctor, really I wasn't. You're not any fun after all. You've got rules, morals, restraint, all so very dull. But when you practically pushed your companion into my lap, how was I supposed to resist?" He gave a malicious grin, sending shivers down Molly's spine. "I really don't see the thinking here, Doc. You could have any number of geniuses as your companion, and you chose little Molly Hooper."
The Time Lord gave a little shrug. "Genius can be overrated," was all he said. His eyes narrowed as he asked, "What's the point of all this, then? Dragging us out here, two geniuses. Are you just here to show off?"
Before Moriarty could respond, Sherlock provided an answer. "It's a distraction. The whole elaborate dance, all the games, all just a distraction, to keep me from finding this."
Slowly, he held out a flash drive, offering it to Moriarty, who took it with interest. "Ooo, the missile plans." He looked down at the little flash drive for a moment, then looked up with a grin that clearly said suckers! "Bo-ring! I could've gotten them anywhere!"
He went to toss the flashdrive into the pool, and for that crucial moment, his attention was elsewhere. Molly had barely processed this when John utilized it, grabbing Moriarty from behind and using his as a human shield against the laser dots. "Run!" he gasped out, but no one moved. Molly still had a bomb strapped to her, and she wasn't leaving anyone behind, even if she didn't know John very well. Not after Frank.
Moriarty let out something of a strangled cry as John wrapped his arms around his throat and chest, but he didn't seem angered by the turn of events. Instead, he seemed almost delighted. "Good! Ve-ry good!"
John struggled to keep a firm hold on the taller Moriarty, though the man wasn't actively trying to get free. "Your sniper pulls that trigger, Mr. Moriarty, and we both go up."
Moriarty looked back at John appraisingly, acting remarkably calm for someone being used as a human shield. "I can see why you like having him around. But then, people always do get so sentimental about their pets, am I right Doctor? So touchingly loyal. But whoops!"
Slowly, the dreaded red dots made their way to Sherlock, dancing tauntingly across his forehead. "I think you've rather shown your hand there, Doctor Watson." John released Moriarty immediately, backing up so he was out of range. The small hope that Molly'd felt faded. There'd be no tricky escapes; they'd have to play this game through to the end.
Moriarty straightened his slightly ruffled coat, dusting it off over-dramatically. "Westwood." He looked up at Molly with a knowing smirk. "Oh, and Molly dear, in case Johnny boy gave you any clever ideas..."
Red dots appeared on the Doctor's forehead, and on both sides of his chest, over both hearts. Molly's breath caught at the sight, but the Doctor just scoffed. "You really think a gun can kill a Time Lord? You should have done your homework better."
Moriarty shrugged unconcernedly. "I'm told it hurts like hell, though. And let's remember, sweet little Molly's not so invincible, so no tricks now alien boy."
The Doctor's expression darkened at the threat. "Why are you doing this?" he bit out through gritted teeth. "What's the point?"
Moriarty gazed back calmly, growing dangerously calm. "A warning," he replied simply. "Sherlock's been sticking his nose in where it really doesn't belong, and you have a bit of a track record for interfering. A consulting criminal with a extensive network has to watch his back. I've brought you here to make a point. I've shown you what I can do, I cut loose all those people, all those little problems, even thirty million quid just to get you to come out and play, so take this as a friendly warning, my dear. Back off."
"Not likely," the Doctor told him in a low voice. He took a few slow steps toward Moriarty, dangerously still. "You still haven't done the research, have you? Because there's a name for me out there. The deadliest race in the universe gave it to me, and the last time they tried to use my companion as a bargaining chip, I turned them into dust. So never think that you can hurt the people I care about and get away with it, because greater people than you have tried and failed!" His voice had gained volume by the end, heavy with rage.
Moriarty seemed completely unruffled by the Doctor's tone. "You seem to be under the impression I'm only threatening Miss Hooper." The color drained from the Doctor's face as he took in his full meaning, and the monster's smirk widened. "You think I didn't walk into this meeting without reading through your files? Companion after companion after companion, you busy boy, and most of them conveniently enough living on Earth, completely oblivious about little old me. Jo and her darling husband, the Brigidair, dear Sarah Jane... shall I go on? No?"
The Doctor's expression was darker than she'd ever seen it, but he said nothing. He just glared in silence. Moriarty grinned in triumph. "That's what I thought. If you try poking around in my operations, your companions will pay the price, same thing if you tell them about me, you know the drill. Ooo, I might even kill a companion before they meet you! The possibilities of time travel!"
Satisfied that the Doctor was thoroughly warned, he turned back to Sherlock. Molly got the feeling he'd only wanted the Doctor out of the way because of the threat he posed. It was Sherlock he was really interested in, Sherlock he saw as his equal. "Do you know what happens, Sherlock, if you don't leave me alone? To you?"
The detective looked almost bored with the cliche. "Oh, let me guess, I get killed."
Moriarty's eyes widened. "Kill you?" he repeated with distaste. "Well, well no, don't be obvious. I mean, I'm gonna kill you anyway, someday. I don't wanna rush it though. I'm saving it up for something special. No, no, no, no. If you do not stop prying... I will burn you." His voice had gone eerily serious, his gaze intense as he watched Sherlock. "I will burn the heart out of you."
"I have been reliably informed that I don't have one." Molly saw a slight hint of guilt flash on the Doctor's face, which confused her. What had he said to Sherlock after she'd left? John was looking more guilty, sending an apologetic look to Sherlock from where he stood.
Moriarty just smirked. "But we both know that's not quite true, is it?" He looked pointedly at John; Sherlock followed his gaze with fear evident in his eyes. It shouldn't have hurt. It really shouldn't have hurt that much, seeing that Sherlock cared more about John than her. She'd known and accepted it. But it still hurt to see the fear when John was threatened, and the way he completely ignored her, though she was in the same danger.
The monster's gaze slid lazily between the three of them, seeming in no hurry to say anything more of import. Then he shifted, straightening slightly. "Well, I better be off. It was so nice to have had this little chat." He turned to leave, strolling off with a completely casual air.
"Wait." Moriarty paused, turning slightly to look back. It was Molly who had spoken; there was something that had been nagging her from the beginning, something that didn't add up. She fought to keep her voice level as she asked, "Why are you doing this? What are you after? Money, power, what? What are your operations for in the first place?"
Moriarty turned fully to face her. She had faced metal Daleks, cruel-faced carionites, vicious pigmen, and they had all been dangerous and frightening in their ways. But the grin on his face was somehow a whole different type of horrible. His eyes were completely cold and empty, and his grin seemed to only make every line on his face sharper. He waited a few moments, then spoke one word that sent shivers down Molly's spine. "Fun."
He turned back to the two non-hostages. "Ciao, Sherlock Holmes, Doctor." With that, he began sauntering off again.
Sherlock followed him for a few steps, gun still pointed level at Moriarty's retreating figure. "Catch... you... later."
Moriarty disappeared behind the doors of the pool, but not without giving a last parting, sing-song shot. "No you won't!"
Molly let out the breath she'd been holding, feeling almost light-headed with relief. It was over. It was really, truly over. For now, at least, they were safe from the maniac who'd lied to her.
Sherlock bolted straight for John, but Molly found herself running right for the Doctor. She went in for a hug, but he focused on her bomb vest first. They worked to rip it off together, then he quickly rendered it harmless with his sonic screwdriver.
Letting out a relieved laugh, the Doctor pulled her into a tight, crushing hug. She hadn't realized she was trembling until she felt the Doctor's arms try to steady her. "You alright?" he asked a little breathlessly.
Molly gave a little, relieved giggle. "I'm fine." The tears she'd held back all day were in free-fall now. She fought to choke back a sob, pulling tighter into the hug. "Thanks for coming for me," she mumbled into his coat.
"Always," the Doctor promised firmly, grip on her tightening. There was something off about his tone.
The pathologist pulled back, studying the Time Lord's face. Of course. Moriarty's threat to his past companions. "I'm sorry for getting you into this, and for what Ji- Moriarty said."
The Doctor's expression hardened slightly. "That wasn't your fault," he told her firmly.
Molly smiled sadly at him, tears blurring her vision a bit. "You heard him," she said dully. "If it wasn't for me, he wouldn't have come after you and your companions in the first place." Now that the relief was fading a little, the horror was setting in. Jim, sweet Jim, had used her as bait for her only real friend. He'd used her, lied to her, forced her to say hateful words about herself. She dipped her head, trying to hide the torrent of emotions.
She wasn't fast enough for the Doctor, who saw her expression and pulled her into another tight hug. "You are my companion, Molly Hooper. Got it?"
She didn't answer; she couldn't. All she could do was cling to her best friend and try to get her mind through what had happened.
So here's the end of the Great Game. It's kinda long, and I didn't include the bit about him coming back since it didn't happen this time. There will be another interlude, then moving on to 42.
As for his past companions - yes, Moriarty went there. And yes he also decided to be as much of an asshole as he could to Molly. I will be dealing with the past companions as little as humanly possible, since I've never seen Classic Who and don't know anything about them. The little I've included here comes from what I read off the TARDIS wiki.
I hope I got the dialogue and feel of this scene right. This is a seriously intense, difficult scene, and adding in two extra characters has the potential to really ruin it. I hope I didn't.