The Doctor

He's like fire and ice and rage. He's like the night, and the storm in the heart of the sun. He's ancient and forever. He burns at the center of time and he can see the turn of the universe. And... he's wonderful

-Tim Latimer

At breakfast, Clary sat awkwardly at the table, trying to not to aggravate any of the cuts. Jace was in the kitchen, making toast and pouring bowls of cereal for the two, and his eyes never left Clary. It had been a hard night; Clary had stayed up late, sobbing into his shirt while he ran his hands through her hair, unable to rub her back. When she finally dozed off, Jace relaxed onto his back only to be woken a few hours later to her strange, strangled screams. He'd had to coax her into the fetal position, kissing her hair and cheeks. Neither of them had gotten much sleep.

"You should eat before we go," said Jace as he placed the bowl and plate down before her. "It'll make you feel better."

Clary stared at the bowl before her, feeling miserable and helpless. "What's the point, Jace? I'm better off dead."

Jace's face paled. "Don't you dare say that," he said softly but with conviction that turned Clary's eyes on him. "I told you-I told you all night-you're not worthless. You can't listen to Valentine because this is what he wants. He wants you to feel this way."

"But he's right," she whispered. "What do I do that's worth anything?"

"You love me," he said, dropping his eyes for a moment. "You're the first person, Clary, to love me like you do. Sure, the Lightwoods cared about me like a son, but you're more than that. You make me feel like I'm wanted."

"Because people want you," Clary argued, eyeing him jealously. Jace was a handsome, gifted, charming shadowhunter; of course he was wanted. "You're useful, at least. Valentine raised you and didn't hate the sight of you."

"You don't know that," laughed Jace darkly. "He wasn't exactly winning the best dad in the world award. As for being useful, you're more than I'll ever be; Clary, you can create new runes. That's impossible, but you do it. You're amazing." She stared into Jace's eyes and felt herself preparing an argument, but Jace silenced her. "But, most important, is that I need you. If you were gone, Clary, I'd be dead. I couldn't bear this place, this life, if you weren't a part of it. I need you Clary, because you're the only reason I have to live. You give me reason, a purpose. I'm worth it, aren't I?"

"Yes," Clary murmured into her breakfast after a moment. "Yes, you are."

After that, Jace refused to have any more conversation about it. He sat with Clary in the bathroom as she carefully applied make-up to cover the cut on her cheek. She looked helplessly on the burns on her chest and arms and chose a long-sleeved, scoop-necked shirt. Before they left, Clary made sure her hair hung to cover the burns on the back of her neck.

At school, Jace and Clary were silent. They didn't lift their eyes. They didn't participate in class. They could have been dead for all the world knew, but for their beating hearts. Clary caught a few eyes resting on her, and she panicked, thinking they might have spotted a burn. A few girls whispered how odd Clary was, and few boys thought that Jace had done it and considered reporting him.

When they finally came to math, Clary and Jace's now most hated subject, the Doctor was waiting for them with gleaming eyes. His eyes raced over Clary and Jace, and he felt his hearts beat a little oddly. There was certainly something wrong with them, and Clary kept tugging listlessly on her shirt collar. He guessed that whatever he or the other teachers had revealed about Jace and Clary's school work had not been met well at their home.

"Welcome students!" Mr. Smith cried, spreading his arms wide like it were a treat. "I hope your parents were all pleased." There was some grumbling among the students, but Jace and Clary remained stoically silent. Mr. Smith seemed to be, as always, blissfully unaware of any discontent. "Shall we get started on some math?" He, at least, sounded excited.

Mr. Smith set to writing on the board again, and Jace watched him, his eyes narrowed bitterly. He blamed Clary's punishment on the man, blamed him for being stupid enough to mention tutoring, blamed him for being so delightfully pleased with the world while he and Clary were condemned to hell. Part of Jace wanted to throttled the man, shake him still he understood.

You mindless, stupid, bow-tie wearing Mundane, thought Jace furiously. His eyes went irrevocably to Clary, who was seated, watching the board desperately. You have no idea what you've done, what you're doing to us. I hate you.

"Mr. Lightwood," Mr. Smith called, as if sensing his anger. "Would you care to answer the question on the board?"

No. "Yeah, sure," he shrugged and went to the board. Jace scribbled out an answer, hoping his calculations were correct.

Mr. Smith eyed the board. "Very nice." He winked at Jace, hoping to raise some sort of emotion from the boy, but Jace just stared back blankly. The Doctor swallowed back any more comments, and gestured Jace back to his seat; he was going to have act today.

"So, as you can see, Jace's calculations were correct and…" Mr. Smith continued to speak as the class became more and more catatonic. It wasn't that what he was saying was boring or pointless, it just seemed that way for a class full of high school students. He assigned problems and began his usual wander among the class, checking their work. He drew closer to where Jace and Clary were working.

"You two are being awfully quiet. Cat got your tongue?" he said with a winning smile, then his face dropped as he considered his words. "Well, not necessarily a cat, since they're not exactly known for eating tongues. Does make you wonder where the saying cropped up from, doesn't it? Cats eating tongues…" the Doctor made a strange face, sticking his tongue out and scrunching up his nose. Clary wanted to laugh, but her burns ignited pain down her sides, and she pressed her lips together. "Anyway, I was hoping to get a word with you two after class today. It'll be quick, just some concerns your father raised I thought might discuss with you."

"We really can't be late to English-"

"Don't worry about it," said the Doctor waving his hands rather madly. "I'll write you a pass to class. But this is actually very urgent, very important. It will only take a few minutes at most, just a few minutes."

Clary looked over at Jace wanly and said, "We'll stay. I'm sure my father will want to know anything about our grades." As she said it, Clary felt her heart drop; she wasn't sure how much more of her father's anger she could bear.

For the rest of class, Jace and Clary sat in silent misery. They had both assumed that whatever Mr. Smith had to say to them would get back to their father anyhow, and once it did, they wouldn't hear the end of it. Jace eyed Clary from his desk and decided that whatever happened next, no matter how bad it got, he was going to protect her. Clary was staring around the room with empty eyes, shaking a little bit against her will; she looked ready to fall apart. Jace knew she was strong, but Valentine's anger was breaking her.

As the lesson came to a close, the Doctor kept his eyes fixed on Jace and Clary. Part of him worried the children might simply go, and after Amy and Rory had returned from the Institute, their minds racing with what the Lightwoods had told them, the Doctor knew he couldn't let the shadowhunters return to Valentine. Students filed out as the bell rang, but, as requested Clary and Jace remained behind in their seats. Clary watched the others go dejectedly, wishing that her life could just go back to the way it was before Valentine had come. She slowly turned her eyes on Jace to find that he was staring anywhere but at Mr. Smith.

It must be miserable when you're used to being the best, to suddenly be the worst, mused Clary, thinking of Jace's life of training.

When the last straggler left, the Doctor snapped the door shut. He paused a moment, trying to think of the right way to introduce the frankly weird subject he was planning on to two disillusioned children. He rubbed his hands together contemplatively. "Right, so, we've got a lot to talk about, and not a lot of time. Alright, we're got a lot time, we've got all the time in world-the universe-but not here, not in this room. I don't store time in a classroom. You'll have to come with me." When the Doctor turned to see how they had taken it, he found Jace and Clary staring back at him blankly. He adjusted his bowtie, waiting for them to say something. "I'm being serious, you need to come with me; I can take you anywhere, but not while we're in here."

Jace, who found his voice first, seemed to only understand one thing the Doctor had said. "We need to go with you?" he asked, feeling like his mind was clouded.

"Yes, right now, actually, before the principal comes down here; he said he wanted to have a meeting with me over the ninth grade math classes." Mr. Smith smiled widely at them.

"Go with you?" repeated Clary faintly.

"Yes," said the Doctor. "Go, to leave, abscond, push off, push on, vamoose, and, my personal favorite, to take flight."

"We can't," said Clary after a beat. "We have to go home after school."

The Doctor leaned against the door, crossing his arms, and giving them a long look. Jace saw, for the first time, something in his eyes that made him shiver. He had felt from the first that Mr. Smith was not wholly human, but now, he felt it tenfold. His hairs stood on end, and though he didn't quite feel fear, he suspected it was only because he'd never seen Mr. Smith angry and was so confused by the man in the first place.

"Do you really have to go home?" asked Mr. Smith softly. "Do you want to go home to Valentine? I get the impression from that man that he's not going to be winning Father of the Year anytime soon."

"He's very good to us," Clary said as firmly as she could, considering the repercussions if she failed him.

"Good to you?" asked Mr. Smith sharply, and he pulled himself from the wall with that same chaotic energy he'd had on the first day of class. "Is his goodness to blame for your nervousness, your silence, those shadows under your eyes?"

"We're fine," Jace repeated, and he put all the strength he could into his voice.

"I'm not a fool," Mr. Smith said darkly, considering his next words. "I know Valentine isn't your father Jace, he's not even your father, Clary, not in any real sense. You'd probably prefer Luke."

Clary felt the color drain from her face, her mouth moving against her will. "L-Luke? I don't know any Luke, you've got me confused for another student-"

"Luke, you know, the guy with the fur problem about once a month?" Mr. Smith waved his hand over his own body. "I can only imagine why Valentine doesn't want him around, seeing as your mom practically lived with him. I get the feeling Valentine is the jealous type."

"Stop this," Clary said, terror gripping her. If Mr. Smith knew this, it was going to get back to her father, and her father would blame her and he would punish her. "Stop talking."

"But then, Valentine always hated those-what did he call them?-Downworlders." Mr. Smith had joined them at their desks, and his eyes were far away on another memory. I suppose he's had most of them executed since he summoned the angel?"

"Stop talking!" Jace snarled suddenly, lunging to his feet. Mr. Smith started when Jace turned on him, his eyes widening and taking a nervous step back. "Just stop talking. You're not helping anyone with it!"

"I'm trying to help you if you'll let me," said Mr. Smith gently, holding up his hands. "Let me help you, just come with me and I can fix everything."

"You'll fix nothing!" Jace spat, griping Clary's shoulders to calm himself. "We don't want your help, we don't need it. All you're doing is making things so much worse."

"I can make everything better, just listen to me-"

"Stop, stop, stop!" Clary cried, jumping to her feet. "I don't know who you are, I don't know how you know what you know, but just stop. Valentine will be furious if he ever knew. We won't say anything to him, I swear, but you have to leave us alone."

"Listen to me!" Mr. Smith ordered, and though his voice was soft, it was hard as steel. "I can help you, I can make everything better, but you have to trust me a little. I know it sounds impossible, I know you think I'm lying, or you think I'm some crazy Downworlder or something, but I'm not. I'm much better than anything you could possible begin to imagine."

Clary laughed hoarsely. "There's nothing you can do."

"Isabelle says otherwise," said Mr. Smith simply, and carefully, he reached into his tweed coat and removed the golden whip. It was curled up in its bracelet form, but Jace, who had seen that whip for years, recognized it at once. He felt his mouth hang open and he quickly snapped it shut.

"What did you do to her?" he hissed, and then drew Clary back into his arms. "Are you working for Valentine? Is this just some sick test-"

"I'm not working for Valentine," said Mr. Smith, looking thoroughly disappointed. "Trust me, he wouldn't want a man like me in his retinue. I'm not what you would call…human." He shrugged as if the entire concept of being human were overrated.

"You're a Downworlder?" Clary asked. "You've got some nerve, being a teacher to Valentine's children."

"I'm not one of those either," said Mr. Smith, and his eyes dropped like a guilty child.

Jace had raised his eyebrow, but the sight of Isabelle's most prized possession in Mr. Smith's hand urged him on. "Really, so what are you?"

"Well, I mean to say, it's a little complicated." Mr. Smith cupped his hands together, bending over a little, and walking around in a possessed manor. Clary was reminded of the books she'd read of Sherlock Holmes; of his pacing manner and his self-possessed wisdom. "See, I'm not exactly from this…planet, technically," he said quickly. "I'm more of a visitor, a guest, a frequent caller, if you will."

"You're not from this planet?" Clary said, unable to stop the sarcasm that tainted her tone. "Yes, that makes sense. An alien from another planet has landed in New York, completely unnoticed, and he happens to be a calculus teacher as well. Gosh, I've been silly."

"Well, you know," said Mr. Smith, "you're the one who thinks an angel arrived on this planet, mixed his blood in a cup with yours, and somehow, made a new species. That sounds about as far-fetched as me being from another planet."

"You really think we're going to believe this?" Jace said, and a smirk curled his lips.

"No, not really," agreed Mr. Smith, suddenly happy. "Most people don't till I give 'em a spin on my Tardis, which, consequently, I'm more than willing to do for you. However, that involves us getting on the Tardis, which, as I've said, we need to do soon. Time is of the essence here, well, when I say here, I mean this literal place," he gestured down at the ground as if he couldn't help but move, like energy was bursting from him. "Once we get on the Tardis, things will be different."

Clary blinked and shook her head. "What are you talking about?"

"My Tardis." Mr. Smith spun about to face her, his eyes glittering and he took off speaking faster than Clary or Jace could really understand. "She's beautiful, wonderful, the most powerful ship in the universe! The engine is a perpetual supernova-The Eye of Harmony, allowing her to travel through time and space at will. She's infinitely huge on the inside, got everything you could possibly want, I promise you that, and if she doesn't have it, she'll make it. Libraries, pools, tennis courts, toy rooms, bedrooms, the possibilities are endless. Did I mention I time travel?" He jumped as if he'd said something that had even surprised him. Jace's face had finally given way to confusion and Clary's mouth was hanging open. "I do, I travel through time, I'm a Time Lord." He seemed embarrassed by this.

"You're mad," said Jace weakly. "You don't work for Valentine, because you're mad."

"Well, maybe," admitted Mr. Smith. "Madness and brilliance have always seemed to go hand-in-hand as far I've seen. Do you think one negates the other?"

"Where did you get the whip from?" demanded Jace, turning the subject before they lost track. "What did you do to Isabelle?"

"I didn't do anything to her. Amy brought this to me, said Isabelle told me to show it to you so you would know she was behind this." When Jace continued to glare, Mr. Smith sighed. "Amy, you know, the red haired woman you met who said she traveled with me?"

"Where did she meet Isabelle then?"

"At the Institute," shrugged Mr. Smith, and then he pressed his face against the door, peeking out a crack in it. "Alright, the principal is almost here, and we haven't got time for this. Please, just trust me. I'll help you, I'll make everything all right." He saw the guarded expressions on their faces and ran his hands through his hair and spoke slowly. "I'll protect you from Valentine, I swear I can. No matter how powerful you think he is, no matter how much control he seems to have, I swear I can take you places he can never reach. I can make sure you never have to see him again."

"But you can't," Clary whispered. "He can track us, he can order us back to him, he'll hunt us down. There is nowhere, no way, you can help us. It's impossible."

Mr. Smith's face fell and, to Jace, he seemed suddenly immeasurably sad. He rushed over to Clary, taking her hands in his, and Clary felt a strange rush of energy and strength burst through her. "You can trust me to help. I am and always will be the optimist. The hoper of far-flung hopes. The dreamer of improbable dreams." He brushed his thumb over Clary's cheek and she felt like a little girl again, looking up into the eyes of Luke. "Trust me to help you."

"Okay," Clary whispered, hoping beyond all hope what Mr. Smith was saying was true.

As Mr. Smith led Jace and Clary away from the school, he was speaking to them, muttering really. It was a steady stream of words that didn't really make much sense to the two shadowhunters, he kept going on about the Tardis, and the time vortex, and paradoxes. Once in a while, he would turn around and tell Clary he was going to fix everything, or tell Jace that he was going to be amazed beyond his wildest dreams. As they went, they earned a few confused stares, mostly because Mr. Smith was dressed so oddly and Jace and Clary looked so forlorn. Then, Mr. Smith rounded a corner to an alley and spun around, throwing his arms up like a conductor.

"Isn't she beautiful!" he cried, smiling widely at the two. When they looked back at him with empty eyes, his face fell a little. "I mean, sure, she doesn't look like much from the outside, but wait till you look inside-"

"That's a phone box," Jace said, bored and tired. "You've led us to a blue phone box down a secluded, questionable alley. Clary, he's insane."

Clary stared at the blue phone box and decided at once that she liked it. Maybe it was because it looked so sweet, so perfectly out of place, but Clary was reminded of London in the 60's for some reason, and it was a balm on her recent hectic life. Besides, that's a pretty blue, she thought. "How can you travel through time and space with a married couple in a small, blue box? How do you fit?"

"Well, it's hard to explain when you don't understand physics," shrugged Mr. Smith.

"Why is there a light on top?" asked Clary, staring at the small light. "Do you change the bulb often?"

Mr. Smith burst into laughter. "You're not the first red-head to ask me that." He wiped his eyes and then gestured to the blue box. "Come along, shadowhunters, come along. Once we're inside, everything will be fine."

"Mr. Smith," Jace said, his voice taut as a wire, "we can't all fit in there."

"Please, Jace, my name is not Mr. Smith. You can call me the Doctor."

When the Doctor threw open the doors to the Tardis, Clary and Jace felt a rush of wind blow back their hair, and they heard the Doctor's footsteps as they echoed off a metal floor. Gradually, the shock of what they were staring at wore off long enough for them to take a step over the threshold of the Tardis and into the control room. The Doctor was running around a huge tower that, to Clary and Jace, seemed to be alive and glowing. As soon as they were in the Tardis proper, the doors swung shut with a snap and Clary stumbled away from them, Jace catching her. Their eyes left the closed, oddly wooden, doors and traveled up the wall. They tried to see the ceiling, but it seemed to vanish into impenetrable darkness. Clary felt dizzy, so she looked down at her feet only to see the grating, and below that, a strange blue light. Clary's heart started to pound and she saw across the room, a staircase that led off down a hall with the same blue light.

"It's huge," Clary whispered weakly against Jace's chest. "Jace, it's huge."

"It's impossible," Jace breathed back. "This is impossible. You can't have a dimension just locked up inside another one. You can't."

"What do you think?" cried the Doctor. "Amazing, isn't it? Please, feel free to make yourselves at home. Hang your coats up." He pointed to the coat hanger behind them

Jace whipped around to the coat hanger and stared. It was the placement of this perfectly normal, perfectly mundane, object in the middle of a time machine that finally got to him. He'd seen too much in such a short time, suffered too much lately; his nerves were frayed. When Jace turned back to the Doctor he knew he was looking at something that wasn't human, something that wasn't even from this world, and that scared him more than cared to admit. This thing was capable of fitting another dimension in a box, he could travel through time and space. He seemed to be infinitely capable, infinitely dangerous.

"You're not human," Jace accused.

"I told you I wasn't," laughed the Doctor, and he jumped back down to meet them. "I find being human to be slightly overrated, don't you think? I hope you believe me now, now that you're safe and sound in the Tardis."

"We're not safe," Clary said, narrowing her eyes at the Doctor. She jerked back her sleeve to reveal her wrist and the Mark her father had placed there. "My father did this, it's a tracking rune. He'll hunt us down the moment he doesn't see us after school."

The Doctor gently turned her wrist over, his ageless eyes glancing over the Mark. "Impossible," he announced. "You're in the Tardis now, in a different dimension. The interior of the Tardis is in a state known as temporal grace. Technically, anything inside the Tardis doesn't exist. You don't exist while in here, so how can Valentine find you?" He was smiling again, and Clary hoped that same unbelievable hope. "Besides, nothing gets through those doors, nothing. No shadowhunter, no demon, no angel, and trust me, they've all tried before." Something in the way his voice changed told Jace he was speaking the truth. "Come along, I'll show you around."

Jace placed his palm on the small of Clary's back and the other on her shoulder and began to lead her after the Doctor. Their eyes strayed from the Doctor, glancing off the hard metal interior, and they thought how cold and empty the Tardis was, ignoring the life that seemed to be thrumming through it. Clary slowly turned her eyes back on the Doctor and he was fiddling with knobs, flashing lights, pushing buttons on the counsel. When he saw her looking, the Doctor suddenly smiled.

"You're inside the largest, most-powerful ship in the universe. She's a bit picky, but she's been around for a long time, and she always seems to get me where I need to be."

"It's so big," breathed Clary again.

"How do you trap another dimension within the other?" asked Jace starkly.

"The Tardis is dimensionally transcendental, this means the interior is a separate dimension from the exterior. It's a little complicated to explain; Time Lords were the only ones as far as I know to understand transdimensional engineering. But, that's how it's done," he shrugged, as if the entire idea of dimensions in dimensions were mundane. "I can show you to your rooms if you like, or the library, or maybe the pool or-"

Clary had been listening to the Doctor and she felt her heart start to beat faster. Even though he was talking, even though he sounded reasonable and pleased, Clary thought that it was all too much. She tossed Jace's hands off and she rounded on the Doctor.

"Stop talking, just stop talking!" Jace tried to grab her, terrified she was going to get herself thrown out. "This doesn't make any sense, everything you're saying-it's crazy. It can't happen, none of this is real!"

"Well, I said that," nodded the Doctor.

"Then why are you lying?" Clary demanded. "Why is all of this a lie? This place can't be real, I'm not safe. We're not safe." She turned on Jace just as he managed to pull her back. "Stop it, Jace. You know I'm right, you know it's not real." She sounded desperate, almost crazed.

Jace's eyes darted up to the Doctor, and he was surprised to see the man was looking confused-not angry. "Clary, it's real, it's all real, just a little confusing…"

"No, it can't be real," Clary shook her head determinedly. "You said it yourself!"

"Help me," Jace hissed at the Doctor, who was still looking anxious and confused.

"What am I supposed to do?" he said, his voice adorably like a young boy's. He waved his hands at Jace in a shooing gesture. "You're her boyfriend, you do something!"

Clary screamed again and tried to worm her way out of Jace's arms when a door slammed above them. Amy and Rory were watching the struggle and Amy rolled her eyes. "Never leave the boys alone." She tripped down the stairs easily and came over to where Jace was holding Clary. She helped Jace lead Clary to a seat and sat her down, enfolding the girl in her arms. "It's okay, Clary," she cooed. "Try to breathe, try to focus on breathing. I know it all seems crazy, you should have seen me the first time on the Tardis…" Amy continued to speak softly to Clary, and Jace was impressed to see that Clary was gradually relaxing into her arms.

Maybe it was the patient rhythms of her voice, maybe it was that Clary had gone so long without an adult woman in her life, but she broke down into sobs in Amy's arms. Clary felt, for the first time in months, that she was being cared for, maybe even loved. Amy was holding her, enjoying the feeling of a small, warm body in her arms, and she rubbed her back comfortingly.

"Who are you?" Jace asked sharply, eyeing Rory. He didn't see much to the man, just a nervous looking Mundane. "You don't look like much of a time traveler to me."

"I'm Amy's husband," Rory said, and, though Jace felt Rory's eyes on him, he didn't know Rory was looking at the way Jace held himself. He looked wary, like an animal that was cornered. "I'm Head of Nursing at a hospital."

"A nurse, a model, and an alien," Jace said darkly. "This makes sense."

"You get used to it after a while," Rory said in an offhand sort of way. "I thought it was all bit crazy at first, you should have seen what it was like first time out. Let me tell you, space fish…" Jace gave him a strange look but then turned his attention back on Clary.

Clary was still sobbing, and Amy could feel her body shaking in her arms. She tried to calm the girl down, rubbing her back. As her hand made small circles on her back, Amy pushed Clary's shirt up, and her fingers brushed over scared tissue. Amy's eyes widened in shock and Clary stopped crying at once, her back straightening and her gaze shifting up.

"Clary, what is this?" Amy asked, and Jace's heart skipped a beat. "Are you hurt?"

Rory had moved at once to Amy's side, but Clary jerked herself out of Amy's arms. "It's nothing, it's just a scratch." Her eyes went to Jace, imploring.

"Clary, you have scars all over your back," Amy said, pushing the hair out of the girl's face. "What happened to you? Who did this?"

Amy's concern must have alerted the Doctor, who had joined them. His face, for once, was looking uncharacteristically serious, his eyes dark with age and something else. "It's nothing," Jace said again.

Rory was trying to take a closer look at Clary's back, but Jace's sudden outburst had drawn his attention. "Who did this? This isn't accidental."

Jace pressed his lips together. "We have to go," he said swiftly. "Clary and I need to go back. We're in enough trouble as is."

"You're not going back," said the Doctor, and his voice was stern. More stern than even Valentine had ever sounded. "I brought you here to protect you-apparently from this."

Clary was looking panicked, her eyes racing between Jace and the Doctor, her hands clutching desperately at her shirt. "Jace is right," she said weakly, but she was shaking under the Doctor's cold look and Amy's sympathetic eyes.

"Let us help you," Rory said gently, rubbing her shoulder. His eyes moved over to Jace who was pale and nervous. "Let us help both of you."