Bonds of Time

by Tardis-Version 3

Time. That's the only thing that the Doctor has. Time. It's what the Doctor has been through and what is in store. Follow the Doctor and the return of Martha Jones as Time gives them a second chance. However, Time may be kind... but Fate is cruel. ON HIATUS: Not abandoned by any means

1. Facing the Past Part 1

Doctor Who- Bonds of Time

Hi everyone. Before I start, I would like saying, or writing, a few things. Firstly, thank you all for taking the time to read my first fan fiction. It really means a lot to me, as I am an aspiring writer. I would also like to thank my friend KobraFists for encouraging me to write. If you feel like reading a Skulduggery Pleasant fan fiction, check it out. It's the least I could do for him. Anyway, I'm going of the topic. Here are the names for the 'episodes' in my fanfic:

-Facing the Past

-Turbulence

-Angels and Demons

-Pest Control

-Crossfire

-Light as a Feather

-The Pied Piper's Tune

-X= (Doctor x2)

-Protocol 11

-The Cold War

-Dream a Little Dream of Me

-Flesh of the Zygons

-Christmas Special (Name is a secret :P)

-Reign of Stone

-Face of Deception

15 so called 'episodes' each. Let see how this goes. It's almost as much of a mystery to me as it is to you. Oh, and if you like dramatics I have a treat for you. Well, it's not exactly a treat. But for theatrics, while you're reading this story, if you want, listen to this music: .com/watch?v=SKsOr9YdiXM&feature=related. Most of you should recognize it :D So, without further ado, let the story begin. Oh, rated T (possibly M) for later chapters.

Facing the Past:

The Doctor ran across the Tardis's console, jumping up and down like a child in a candy store. His hands darted quicker that the speed of light, pressing random buttons with no idea of their purpose. His favorite, a red lever, had been pulled almost 89 times already. He was 38 percent sure it made the Tardis speed up. He was unfortunately 62 percent sure it was the self-destruct mechanism. But self-destruct mechanisms are big red glowing buttons, so there's no threat there, the Doctor thought, still randomly pressing buttons and squeaking a yellow rubber duck.

" Oh Amy, Rory, you two are going to love Terravaxion 6. The soil is made of diamonds that shimmer like stars in the sunlight. Of course, the Oximorn, or 'space cow' excretes the soil, but once you get past the smell it is actually a nice experience. Manure works wonders for sore feet. So when we…" The Doctor's voice trailed off as he realized the Tardis was empty. He had left Amy and Rory so they could be safe. A wise choice, he knew, but not one he was happy with. He sat down, and took out his Sonic Screwdriver. He twirled it in the air once, then just put it back in his pocket. The Tardis whirred and the Doctor looked up.

" I know I've always got you Sexy." The Doctor said quietly, stroking the Tardis. " But you're a sore substitute for company. I mean, you're brilliant, but you're made of metal. I might as well be travelling with a Cyberman." The Tardis whirred angrily, and the Doctor shook his head in disbelief.

" Honestly, where do you learn these words? Amy's a bad influence on you." The Doctor chuckled, still surprised that his beloved Tardis had just swore at him and call him a… well, he wasn't quite sure. It either translated to a very bad swear word, or a Buffalo Burrito. The Doctor decided he needed something to take his mind off things, so he opened a panel in the flooring and took out a chest. Good old Blackbeard, the Doctor thought, it was nice of him to give this to me as a gift. Opening the Chest with a rustic key, he looked at his fondest possessions. A mask that used to belong to Adric, K-9's recharge battery, a parchment declaring death against the Doctor by Queen Elizabeth. The Doctor cracked a smile, remembering the Queen in black-laced knickers. Something caught his eye, deep in the chest. It seemed to shine slightly, and the Doctor picked it up. It was a photograph of the Doctor and Martha before they had to fight the mutated Lazarus. He smiled at the memory, which had almost been a lifetime ago. In fact, it probably had been. He turned the frame over, seeing his writing. " Wow, my writings pretty good." The Doctor boasted, then sighed as he realized no one was there. " What's the point of being brilliant if no-one can see it?" The Doctor asked, before realizing he was doing it yet again. Closing the chest, but not locking it, he moved over to his couch and started reading out loud.

'To my future self, today was the day I promised Martha to take her to the movies. I swear that I will, because she said I looked good in a suit. Like Agent 0007. Ah Bond, the intergalactic spy. You should remember that. Now, before my ego gets to big I thought that her statement was manically exaggerated. I'll let you be the judge. If I do, you can tell her that she was right, and you'd probably hear the exact words ' I told you so.' Anyway, I thought I would take het to the last Harry Potter movie when it comes out, no cheating using the Tardis. Please take her there."

The Doctor stopped reading from the page. He was a different man now, but he was ashamed that he had forgotten his promise. He only now realized that he had treated Martha like dirt, on the re-bound from losing Rose. " Well, no more I swear. Sexy, set co-ordinates to Earth."

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The first thing the Doctor noticed when he landed was a cement wall. The second thing he noticed was that it was blocking his entrance. And the final thing he noticed was the Tardis was throwing a tantrum. The Doctor decided to use the back door, resulting in a lot of wondering around. Twice, he found himself in the pool area and the Tardis had turned the gravity off. Smoothing down his hair and taking a deep breath, he trudged on, a fish falling out of his pants. When he finally found the entrance, he had to crawl and ended up crawling into the lion cage at the zoo. " Good Cat, Good Kitty." The Doctor soothed, noticing the Lion was angry. " It's not your fault your mom left." When the Zookeepers came to feed the lion, to their utter surprise, they found the lion curled up on the Doctors knees. The Doctor had also activated the chameleon circuit in the Tardis to disguise it to look like the wall. The Doctor got up, and exited the cage with a broad smile. The Doctor dropped by Wilfred Mott's, introducing himself as John Smith and as Wilfred's long lost cousin while Donna was at work. After discovering everything was fine, he departed, his brain taking a trip down memory lane. After just about giving up, the Doctor sat down at a coffee shop on Westminster Avenue. A waitress wearing a maid's uniform and a massive hairdo took his order skeptically, seeing a dripping man in the middle of the store.

" Do you have any fish fingers and custard?" The Doctor asked hopefully, his stomach grumbling like the Tardis's engines.

" Um… no…." The waitress said, looking at the Doctor as if he belonged in an Insane Asylum. The Doctor handed the waitress a fish that came out of his shirt.

" Just use that." The Doctor said smiling, and waved the waitress on. The waitress literally ran back to the counter, tossing the fish randomly, which landed in a sleeping man's coffee. That should be a pleasant surprise when he wakes up, the Doctor thought. Hearing a commotion behind the counter, the Doctor decided he had better leave now. Weighing up his options, he left a 10-dollar tip on the table just to make sure the waitress wasn't offended. But then he realized it would be more fun if she was offended, so he decided to leave another fish on the table, with an autograph. Besides, they really needed fish on the menu. The autograph was for popularity. Leaving the table, he strutted onto the road, feeling quite pleased with himself. Time-Lords needed to have a break sometimes. A shiver ran down his spine as a cold gust of wind began to blow. The Sun seemed to have no heat; no affect on people on what was a 32-degree day only minutes ago. Something's up, the Doctor thought to himself as he scanned the air with his Sonic. It showed a density in the air partials, as if the air itself was clustering together to shelter from something. Out of the corner of his eye he saw a flash of black: a deep, smooth black rushing as immense speed. Turning around the Doctor was knocked off his feet. He felt a prickling sensation in his arm and lashed out with his leg. His arm was throbbing with pain, and he could feel the sensation of warm blood against cold skin. The assailant, caught by surprise, staggered back. The Doctor whirled to his feet to face the assailant. It was a man, well-built and tall, about 8'7. His body was tanned, but every ten seconds it would flash to a deep black colour, allowing his skeleton to be seen momentarily, and then it would change back. No-organs were visible. There was a single prick-point visible on his neck, no bigger than a pencil wound, but it went much deeper. His eyes, a vicious red, were blood-shot. The creature let out a guttural scream, which chilled the Doctor. Some-thing had infected this man, a parasite of some sort. Something that could pass on remnants of its DNA with a single bite. It wasn't a vampire, the Doctor was sure of this.

" My name is the Doctor… I can help you." The Doctor said to the creature. The creature cocked its head as if in recognition. The Doctor put his hand out, which he realized was shaking. Why was his hand shaking? Because for the first time, he had to worry about himself and not others. The creature shook violently, and the Doctor realized what was happening.

" No!" The Doctor yelled, but it was in vain as the creature disintegrated into dust. " The parasite severed the connection." The Doctor said somberly, looking at the remaining ashes. The parasite had killed off the host because the Doctor was going to help it. The Doctor cursed under his breath, that thing hadn't been completely altered. There was still human in it, the longing to be free and normal. But that was what the parasite had wanted. It had a connection, and it falsely promised freedom. Whatever this parasite is, it's clever. Very clever, the Doctor thought to himself. Realization hit the Doctor, and he took a sharp in-take of breath as the pain in his arm finally kicked in. Looking at it, it was badly swollen. Realizing he would have to go to a hospital, the Doctor set off hurriedly, praying that he wouldn't be forced into an early regeneration for something as stupid as an infected wound. Entering the nearest hospital, Sacred Heart Private Hospital using his psychic paper, he entered the emergency room in a rush. Almost sprinting up to the receptionist, who was buried in paper work.

" Hello, I'd like to make an appointment." The Doctor said hastily, wondering why he was re-acting so badly to his wound. The receptionist didn't even look up. She looked about 50, and had graying hair that was kept in a tight crop. Her facial features were slack; as if a sculptor had given up on apiece he was creating. She didn't have, what people called, a friendly face.

" Um… excuse me." The Doctor said, realizing he would have to make his condition sound un-believably urgent. " I'm going to die in 59 seconds."

" Give me a minute." The receptionist said, still not bothering to look up, and the Doctor came to the realization that his efforts to get her attention would have no avail. He had faced Cyberman who weren't as thick as her. He sat down, and surveyed the hospital. It was small, with only two stories. There was a thick smell of hand lotion and antibacterial spray against the godly white walls and furniture. People were sitting down, and looking very ill. Every so often, a name would be called and a patient would go in. They would come out looking sicker than they had been to start with. After half and hour of waiting, the receptionist allowed the Doctor to add his name to the list, and after seeing the massive swelling on his arm, she said that he could go in immediately. The waiting period had had a bad affect on his arm, the swelling spreading to a larger area. It was very dark, as if the skin had been badly bruised. He hoped it wouldn't take too long for it to fix. His clothes were still slightly dripping, and he gathered a few odd looks from the nurses. He was taken to Bed 3, which was decorated brightly with pictures, drawing and a bowl of plastic fruit. He was told to take his clothes off as it would make the bed wet. The Doctor objected, but was literally stripped on the spot by the nurses, touching him in places no one had touched for around 500 years. He had finally had enough when they got to his Goofy underpants. Taking them off in privacy, he wore the fluffy robe they gave him. Though he wasn't happy about wearing it, he had to admit it was comfortable. But he kept the bow tie on. Bowties are cool. Un-able to stand still, he paced around the room till his doctor arrived. He laughed at the thought. His Doctor. Who was the Doctor who helped the Doctor? Who could manage such a task to look after him when he looked after the world? Who was worthy of carrying the weight of that tremendous task on their shoulders? The person that came round the corner answered his questions. Martha Jones.

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The Doctors mouth stood a-gape. This was impossible. There was no way fate, if there was such a thing, worked like this. But then he reminded himself that nothing was impossible, just highly unlikely, and a maniacal grin spread over his face. Martha, for one, was surprised by his reaction. People in hospitals didn't usually smile broadly, they usually moaned in great theatrical pain. Apparently, this man had no need to.

" Oh… this is brilliant." The Doctor said ecstatically, running around in circles with excitement. He clapped his hands, and then looked at Martha's surprised face. " Sorry, I tend to get excited when I see Doctors." The Doctor said, realizing his statement was true. He loved it when he met himself from the past; it reminded him of how brilliant he was and how dull they were.

" That's fine." Martha said, being patient. To be honest, she was actually amused by the man's antics. She had had her fair share of problem patients. " Now, it doesn't mention your name on my list. You would be?" Martha asked, and held back a laugh as she saw the mans carefree expression quickly change into one of sheer panic. She also realized that the man was wearing a bow tie with the fluffy robes the hospital provided. Well, he had a great sense of amusement, but no sense in fashion.

" My name… uh…. It's a long story how I got my name…. ah… My mother gave it to me when I was born…. um…. Actually, it's not that long when I think about it… um… I'm blathering on and on… Did I say my name yet?" The Doctor managed to say. I know all of life's questions, and I can't think of a good name, he thought. He became aware that Martha was staring at him. God, she was beautiful. Must've been 2 years, maybe 3 since he had last seen her. He became aware that he still hadn't said a name. He could just say John Smith. In fact, why hadn't he?

" My name is John Smith." The Doctor said, and Martha looked at him funnily. The last time she had heard that name… She sighed, remembering the Doctor. She had left because she couldn't stand being ignored anymore. Her infatuation with him had been too much; if she had stayed with him she would have become obsessed. She had always been second, longing to be first. So she had left, but she could never forget the blue box that was bigger on the inside. She could never forget the dashing man in the blue suit and she could never forget their adventures. She wondered were he was now. Off saving the universe probably, she thought. She had no idea he was standing in the very same room as her. Writing his name down, she asked him to show her what the problem was. The Doctor, now convinced that she believed his name, showed her the arm. Martha took an intake of breath.

" What happened to you?" Martha asked, staring at the wound. The Doctor, for one, thought it hadn't been so dramatically bad. He looked at it, and instantly knew he was in trouble. What he had initially thought was swelling was much worse. The swelling had stopped, yes, but the middle of his arm was now as black as space itself. He gazed at his arm and saw the puncture, no bigger than a pencil but much deeper. He had been infected. He looked Martha in the eye, and she looked back at him. There was something familiar about those eyes. They sucked you in, showing you their story. Martha saw wisdom…Martha saw pain… Martha saw regret… Martha saw mischief…Martha saw the Doctor.

" That's impossible…" Martha said, her voice barely audible. The Doctor winked at her.

" Hello Martha." He said, and that convinced Martha that he was the Doctor. Her nametag only said her last name.

" That's impossible…" Martha repeated, still surprised.

" There are a lot of things you still need to know about me Martha. There are things a 967 year old hasn't told you. I can cheat death. When I die, I change completely. I… can never die." The Doctor said, and Martha looked at him again. It was him… but he was dead. This man she saw in front of her was nothing but a reincarnation. This man wasn't her Doctor; no-body could ever be the Doctor. She walked up to him and slapped him. He recoiled, and staggered back.

" That's for getting yourself killed." Martha said angrily. She was fuming now, but her harsh barrage of words at the Doctor was cut short by an ear-piercing scream.

" Just like old times, eh." The Doctor said, winking at her, before bolting in the direction of the scream, his robe flapping. Martha, knowing that she had no choice, ran after him.

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(Minutes Earlier) Robbie Manson moaned in pain as his stomach churned. All he had eaten was a bad piece of sushi, and his stomach was burning as if he had eaten a bowl of Chili Soup in once gulp. His stomach grumbled in complaint, and Robbie knew that he was going to spill his guts all over the nice clean floor. To make matters worse, the lights flickered on and off and the air got colder. They must have left a window open, it's chilly in here, he thought but that was the least of his concerns as he felt his stomach lurch violently. He heard his name being called, but right at that moment he felt his stomach upturn. Ignoring the nurse and running to the bathroom, he quickly ran to the nearest cubicle, locked it for privacy, and proceeded to expel his guts. The light in the room dimmed in the room, and the air became cold like Ice. Robbie paid no attention. When he finally finished, he heard footsteps. He barely heard a knock on the cubicle door. " It's occupied." Robbie groaned, feeling very queasy and cold. He turned his back to return to puking, but the cubicle door was ripped off its hinges. A man stood there, holding the door in one hand as if it was nothing. He looked normal, apart from his red eyes and black veins. He also seemed to have two shadows, that didn't follow his movements exactly. He opened his mouth and it grew impossibly wide, before it covered most of his face. A long tongue, which looked like a carving knife, darted out. He let out an ear-piercing scream before he felt a tingling sensation in his chest. He didn't feel or hear what came next, but he could see his blood and flesh splatter all over the walls before everything went black.

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The new Doctor ran quickly, Martha gave him that. He seemed to fly through the air. She realized that she actually liked him. He was different from her Doctor. It was like they were on the same level, but in a different league. The Doctor skidded through the slippery hospital floors until he got to the bathroom. Patients were craning their heads to see what had happened, but no-body bothered to inspect the scene. The nurses would probably be coming soon though, Martha thought. The Doctor almost kicked the door down. What Martha saw made her want to crawl up and cry. It was a skeleton, but nothing like anything Martha had ever seen. Its bones were black and shriveled. But the worse part was that the skin was only missing from the chest upwards. Downwards, the skin and organs lay intact, all shriveled grotesquely and back. Blood and flesh painted the walls in an indecipherable picture of horror and gore. Now she truly remembered the dangers of travelling with the Doctor.

" I'm sorry…I'm so, so sorry." The Doctor said, running his hand down the skeleton. He realized he had seen this somewhere before, a long time ago.

" Martha, get back." The Doctor said, as something fell from the roof. Martha found herself taking quite a few steps back. The man looked human, but he was covered in back veins. He had two shadows, which seemed out of synch with him. The room instantly became colder and Martha saw a thin layer of Ice frost up the window, in the middle of the day. It smiled, revealing a mouth of darkness. Martha thought she caught a glimpse of a tongue, but it was brief.

" Doctor…" It croaked, it's voice raspy. Its eyes seemed to shimmer.

" That would be me, the Doctor, the oncoming storm, the defender of planets. I mean, I can't argue with that. But the question is, who are you?" The Doctor asked dramatically, practically dancing around the room.

" I am T'thakak. But you're primitive language might know me better as the Destroyer." T'thakak said, growling as he did so. His tongue darted in and out. It was covered in strange markings. The Doctor took a step back in recognition when he saw the tongue. He realized what he was up against.

" You're a Gin." The Doctor said, taking a step forward to make sure he didn't look undaunted. " I thought you're kind was extinct."

" The same goes for you, Doctor." T'thakak said taking a step forward. Martha felt an urge to ask the Doctor what that thing was, but she knew that now wasn't the time. She admired the way that this Doctor stood fearlessly, not afraid of a good challenge. " You are infected." T'thakak continued. " Just when I thought you were truly brilliant."

" I have that affect. What decide you to change your mind?" The Doctor replied, and Martha smiled.

" Only people who are tainted of heart become infected. Most just die." Martha's smile faded.

" Well, I'm sure some-one like you should know when some-one is tainted of heart. I mean, look at you. You're whole appearance screams 'tainted!' You're fashion sense is soooooooooo 1589." The Doctor replied. The Destroyer snarled.

" Foreplay is weak, Doctor. I want to rip you limb by limb now, but I could use an asset like you. A creature of pure benevolence, and a creature of pure evil. I'll let you decide which one you are. You and me… we could conquer Earth. Of course, you would be under my command."

" Over my dead body." The Doctor replied, almost snarling. T'thakak just laughed evilly.

" It's a shame… but it can be arranged." He clicked his figures and two infected appeared by his side snarling. The Doctor took a step-back and grabbed Martha.

" Martha…" The Doctor started as the Infected advanced, with only ripping them to shreds of their mind.

" Yes Doctor." Martha gulped, fear over-riding her body. She hoped she would be able to run. Her life hadn't been threatened in 1 year and she wasn't quite accustomed to running for her life. The Infected kept advancing.

" RUN!" The Doctor yelled, and they both bolted out of the bathroom. The Infected let loose a battle cry, and the hunt began.

Thanks for reading the first chapter. Hope you liked it. I didn't pre-read exactly, so mistakes may have occurred. It annoys me that there is a two-day waiting period before you can post stories, but it gave me time to improve the story. Please review, I'll allow anonymous reviews. Expect another chapter in 3 days.

Sincerely, Tardis Beta 1.8.1