Disclaimer: Doctor Who belongs to the BBC. I do not own anything, nor do I make any money from it.

A/N Hello and welcome to a brand new story! As the summary suggests, it will be a AU and sort-of rewrite of the Time War, the 50th anniversary episode and the Eleventh Doctor's regeneration. Basically it is me denying canon and substituting my own.

This first chapter is mostly a rewrite until the very end, but everything after it will be AU based on the hints about the Time War we have got through the show and other theories.

Happy Reading!

Chapter One

When Cass was a young girl, all she could remember was the overwhelming sense of helplessness at her mother's sobs as she told Cass all about her father and how he had died trying to rescue the trapped children in the collapsed school building when Cass had just been a little baby.

That was the thing though. The school would never have collapsed like that if the atmospheric barrier had been holding on Epsilon III. But the barrier had been shattered, the pressure had caused several explosions, particularly in buildings, and countless lives had been lost.

The barrier was rebuilt later, but the damage was done. Epsilon III had officially become a casualty of the Time War. Theirs was a small planet, with not very advanced machinery, and the constant conflicts over the weakened barrier coupled with the Time Lords' destructive delta waves, had left Epsilon III ravaged.

Cass had only waited until she was of legal age, and then she had been eager to leave Epsilon as quickly as possible. She had wanted to be away from it all, see the universe and forget the desolation of Epsilon III, and her mother's neverending sobs.

Though, it seemed like her first voyage was as doomed as her home planet.

"Help me, please. Can anybody hear me?" Cass tried pressing every button on the ship's dash, hoping something or other would work.

The only good it did was having the computer chime back with a request to state the nature of her ailment. It was times like these that Cass remembered the old Earth saying about not trusting any computer you couldn't throw out of a window.

"I'm not injured, I'm crashing. I don't need a doctor," she snapped.

A clear statement of your symptoms will help us provide the medical practitioner appropriate to your individual needs.

Screw throwing it out of a window, thought Cass. I ought to take it apart with my bare hands and trample on its remains. "I'm trying to send a distress signal. Stop talking about doctors!" she said.

"I'm a doctor," came a calm voice from behind her, making Cass whirl around in shock. A handsome man in rather battered clothes was leaning casually against the ship's wall, his arms and legs crossed, and a small smile playing on his face. "But probably not the one you're expecting," he added, walking towards her with quick steps. "Where are the rest of the crew?"

For reasons she couldn't place, Cass felt relief seize her heart. Logically, she knew that she ought to be wary of a strange man appearing in her crashing ship but his presence was soothing, not to mention that he could be her only way out of crashing on some obscure planet.

"Teleported off," she answered hastily, realising that he was waiting for her answer.

"But you're still here," he said, looking at her in surprise.

"I teleported them," she said.

"Why you?" he asked, still in that same tone of surprise.

Cass gave a nervous chuckle as she remembered. "Everyone else was screaming," she said.

A broad smile lit up his face. "Welcome aboard," he said, extending his hand to her.

It was such a bizarre thing to say when the ship they were in was clearly about to crash, yet Cass felt the first beginnings of hope as she looked at him. "Aboard what?" she asked.

He grinned quickly. "I'll show you," he said, pulling her to her feet with the hand she placed in his.

"Where are we going?" asked Cass.

"Back of the ship," he answered.

"Why?" asked Cass, knowing that there were no escape pods there, only an empty bulkhead.

"Because the front crashes first. Think it through," he said, like it was obvious. Before they could reach the exit hatch, the doors hissed and snapped shut as the computer signalled that the bulkhead was now sealed.

"Oh, why did you do that?" asked the Doctor, almost like he was used to berating a misbehaving ship.

"Emergency protocols," said Cass, realisation spreading across her face. She could have smacked herself for forgetting something so basic.

The Doctor didn't look too fazed though, as he drew out a sonic device from his jacket and started examining the sealed doors. "What's your name?" he asked her.

"Cass," she answered, thinking it quite odd how he hadn't even asked her name before helping her. It made her wonder what sort of a man he was that he would jump right into saving someone first and then ask their name later, almost as an afterthought.

"You're young to be crewing a gunship, Cass," he said, glancing sideways at her.

He didn't say it derisively like several others before him had. In fact, he sounded like he was genuinely interested. Not for the first time, Cass wondered if she was in some sort of a bizarre limbo with this strange man while the ship had already crashed.

"I wanted to see the universe," she said, a smile lighting up her face as she remembered the ship flying away from Epsilon III. She had felt truly alive for the first time in her life. "Is it always like this?" She wanted to know, because if so then she was signing up for life.

The Doctor's lips quirked up at her tone, as if he knew exactly what she was thinking. "If you're lucky," he said, just as the bulkhead door slid open.

It was dark beyond it, but Cass could see a box with Police Public Call Box written on it. A sinking feeling started to overcome her, as her smile slipped from her face.

The Doctor saw the fear on her face, but misjudged the reason behind it. "Don't worry," he assured her. "It's bigger on the inside."

Far from being comforted, Cass flinched violently at his words. "What? Bigger on the inside? Is that what you said?" she asked, stepping away from the box involuntarily.

"Yes," said the Doctor, still not having grasped why she was looking so scared and angry. "Come on, you'll love it."

"Is this a TARDIS?" asked Cass, almost as a final confirmation before she signed her death warrant.

The Doctor finally realised the reason for her fear, and could have smacked himself. Of course she was afraid. Times weren't safe, and getting into any TARDIS meant danger beyond comprehension. But not his TARDIS. He knew Cass would be safe in there. "Yes, but you'll be perfectly safe, I promise you," he said, trying to make her understand.

"Don't touch me!" yelled Cass, violently snatching her hand away from his grip, revulsion rising in her throat at the thought of being touched by someone like him.

"I'm not part of the war," said the Doctor quietly. "I swear to you, I never was."

Cass glared at him in disgust. "You're a Time Lord," she spat.

"Yes, I'm a Time Lord, but I'm one of the nice ones," he said, trying to walk towards her.

Cass retreated back immediately, raising her hands as if to defend herself. "Get away from me!" she yelled.

Despite sympathy welling in his hearts, the Doctor did feel some indignation too. "Well, look on the bright side. I'm not a dalek," he said, hoping that his anger would jolt her into action.

Cass took another step back, as his words did indeed jolt her into action. "Who can tell the difference any more?" she said as she slammed her hand on the deadlock seal button. The door closed between her and the Doctor.

"Cass!" yelled the Doctor, already regretting pushing her.

"It's deadlocked. Don't even try," she shouted.

"Cass, just open the door. I'm trying to help," he begged, hoping she would listen.

"Go back to your battlefield. You haven't finished yet. Some of the universe is still standing," she said, her voice cracking as tears began to flow from her eyes.

"I'm not leaving this ship without you," he said, and for a moment Cass believed him. But then she remembered what she had been taught her whole life, the things she had witnessed, the atrocities committed in the name of a higher form of warfare, and a universe left in shambles.

She straightened up and looked him in the eye through the small glass panel between the doors. "Well, you're going to die right here then," she said. "Best news all day."

The ship kept plummeting and Cass closed her eyes, blocking out the Doctor's screams of her name, and the frantic beeping of the ship's systems. For a few moments, it felt so peaceful again, and then everything got very hot and Cass knew no more.

The Sisterhood of Karn were watching their Flame grow smaller and smaller as the war raged over their skies. More Time Lords had visited their planet during the years of war than they ever had before. If the universe had not been on the verge of destruction, the Sisterhood would have refused them access to their Elixir.

As it was, they wanted the Time Lords to win this war. Because Karn's survival depended on it, and Ohila, as the current High Priestess, had no intention of letting the Sisterhood perish.

She had made careful demands from the Time Lords in exchange for the Elixir, and had been watching the timelines constantly. One bright shining timeline stood out to her. It belonged to a man who had helped them before, who held great disdain for the Time Lords, and who had carefully stayed away from this war.

As the gunship broke Karn's atmosphere and crashed to the ground, Ohila's eyes brightened in anticipation. "And here he is at last," she said, a smile gracing her stern features. "The man to end it all. My sisters, the Doctor has returned to Karn."

She took a few tentative steps towards the crashed remains of the ship, and saw a man lying unconscious in the wreckage, "We have always known in our bones that one day he would return here. Such a pity he's dead," she said, her voice hard.

"He's not," said one of the younger acolytes standing behind Ohila.

Ohila looked up at her, startled. "Explain yourself," she snapped.

"He's not dead, High Priestess," said the young acolyte, looking scared. "His hearts still beat and his breath is still strong."

"The timelines were wrong," said Ohila's advisor. "The Doctor will never help us, not in the way we require him to."

"Does this mean we shall perish?" asked the young acolyte, terrified.

"Quiet!" snapped Ohila and everyone fell silent. She was gazing at the Doctor's body with a contemplative look in her eyes. "Take him to the temple, and do not speak a word. I shall deal with this."

As the acolytes scrambled to clear the debris off the Doctor, Ohila's advisor leaned in close to her. "What are you planning, High Priestess?"

Ohila took a deep breath. "We know he is not dead, but he remains unaware of the fact," she said shrewdly. "Is his companion still alive?"

"She's severely injured but the Elixir can…"

"No!" said Ohila immediately. "Let her die."

"High Priestess?"

Ohila inhaled deeply. "Let the girl die," she repeated. "Her death serves a noble cause."

"High Priestess," called her young acolyte. "He's waking up."

Ohila made her way to the temple in quick steps and found that her sisters had the Doctor propped up against the altar. "Quick, fetch the potions," she ordered as the sisters picked up a goblet each and stood quietly in the shadows, praying that Ohila's plan would succeed.

The Doctor was twitching slightly now, his mouth forming silent, incoherent words until a name escaped his lips loudly and clearly as he woke up. "Cass!"

Ohila crouched in front of him. "If you refer to your companion, she's almost certainly dead. No one could survive that crash."

The Doctor looked away at that. "She wasn't my companion," he said. "And I did survive this," he pointed out almost absently as if his mind was elsewhere.

"No," said Ohila, standing up again. "We restored you to life, but it's a temporary measure. You have a little under four minutes."

"Four minutes? That's ages. What if I get bored, or need a television, couple of books? Anyone for chess? Bring me knitting," he said in the same dispassionate tone.

Ohila felt a flash of anger which she tried to tamp down. "You have so little breath left. Spend it wisely," she warned.

His eyes finally focused on his surroundings and a sardonic smile graced his face. "Hang on. Is it you?" he peered at Ohila as he pushed himself to his feet using the altar for support. "Am I back on Karn? You're the Sisterhood of Karn, Keepers of the Flame of utter boredom," he added derisively.

"Eternal life," corrected Ohila, swelling with anger.

"That's the one," he said, still unable to keep the mocking tone from his voice.

"Mock us if you will, but our elixir can trigger your regeneration, bring you back. Time Lord science is elevated here on Karn," she said, bringing the matter to point and the whole reason for this charade. "The change doesn't have to be random. Fat or thin, young or old, man or woman?" she fired off, nodding towards various potions being held by her sisters.

The Doctor appraised her sharply. "Why would you do this for me?" he asked, unconvinced.

Ohila had prepared for that question. "You have helped us in the past," she said.

It didn't appease him. If anything, his eyes narrowed even further. "You were never big on gratitude," he said.

"The war between the Daleks and the Time Lords threatens all reality," said Ohila. "You are the only hope left."

"It's not my war. I will have no part of it," he said as if it was a firm, unshakeable fact.

"You can't ignore it forever," said Ohila sharply.

"I help where I can. I will not fight," he said, anger radiating off him in degrees.

"Because you are the good man, as you call yourself?" It was Ohila's turn to be mocking.

"I call myself the Doctor," he said.

"It's the same thing in your mind," she pointed out with an almost palpable sense of triumph in her tone.

"I'd like to think so," nodded the Doctor.

Ohila smiled bitterly, as if he had said just the right thing. "In that case, Doctor, attend your patient," she said as Cass' body was brought into the temple and laid out on the altar by the sisters.

The Doctor moved at once, scanning her with his screwdriver, hoping for any signs of life. He heard Ohila muttering something about him wasting his time, but all he could see was the eager girl who had wanted to see the universe.

He must have said the last part out loud, for he heard Ohila respond. "She didn't miss much. It's very nearly over," she said harshly.

"I could have saved her," said the Doctor, feeling regret and sorrow fill his hearts. "I could have got her off, but she wouldn't listen." He tried to remember if his time senses had picked up on anything on her life, but all he could remember was a badge of honour for leading the settlement on one of the most progressive colony planets. It had been her future, he realised and then winced when he remembered that it had been cruelly snatched from her before she'd had a chance to fulfil it.

She had been right to hate him, but she should never had died. This war should never had happened but it was happening and he had a part to play. He looked at Ohila and then at the sisters holding the potions. No doubt one of them would possess an elixir to trigger a regeneration that could bear to fight and win the war.

Ohila must have seen his resolve wavering, since she nodded towards the potions again. "Fast or strong, wise or angry. What do you need now?" she asked, nearly desperate in her plea.

The Doctor looked up at her with a gaze as firm as he ever bestowed on anyone. "No," he said.

Ohila seemed taken aback. "No?" she asked. "What do you mean, Doctor?"

"I mean, no," he said, feeling his strength and resolve building.

"Doctor, we stand on the brink of destruction and the end of the universe as we know it," argued Ohila, as if trying to make him understand.

"No," he said, and his voice was like a whip cracking through the silence. "Because this is what I am going to do. I am going to fight in the war, but not as someone stronger, faster, wiser or anything else that you think will make of me. I will fight this war, just as I have every war in my very long lives. I shall fight this war as the Doctor."

"Do you really think a good man can fight a war such as this?" asked Ohila, realising that her plan was falling apart. "Surely a warrior would…"

"The war has too many warriors already," said the Doctor as he looked down at Cass' body. "It is time for me to do my duty, Ohila. What this war needs, is a Doctor."

"Doctor…"

"She deserves a proper burial," said the Doctor, interrupting whatever she was about to say. His mind was made up and as soon as Cass was put to rest, he would willingly walk into the battlefields.

Ohila was quiet but the sisters were looking scared as they exchanged glances. "Very well," she said finally. "We shall see that she finds peace, Doctor."

The Doctor nodded and bowed his head. "Cass, I apologise," he murmured quietly. "But I promise you, this war shall end. I shall end it. For you, and everyone in the universe like you. Farewell, my dear Cass, it is time for you to rest."

His hand squeezed hers briefly before he turned around abruptly and left the temple with quick steps. Outside, he could see the crashed gunship in the distance. As he got closer to it, he realised that his TARDIS was unharmed and standing tall amidst the destruction. The Doctor's steps quickened and he nearly ran all the way back though his feet came to a skidding halt when he realised that there was someone standing next to his TARDIS.

It was a young blonde woman.

A/N Alright, end of Chapter 1. Let me know what it was like.

I anticipate this being around 25-30 chapters and a bit sombre than my usual stuff. Hope you enjoy it just the same. The next chapter will be up soon.