Disclaimer: I really wish I owned this, but I don't, if I did though, brown suit Doctor would not have looked like he did in the last scene in 'Journey's End'.

A/N: Okay this is half way beta-ed, as MissPrufrock has gone on holiday along with her awesome skills. But, I wanted to post this and will edit out the bad bits later, (feel free to point things out as you read). This has become a bit of an epic and has taken over my life, I have an ending written to prove that I can get to that point, I'm working on the middle as we speak. So have at it, and, just in case, the prologue is here: community./timeandchips/5042014.html

They Weren't There: Chapter One

Continuity gives us roots; change gives us branches, letting us stretch and grow and reach new heights. Pauline R. Kezer

Rose walked down the empty street, the sound of her boots as they thudded against the pavement echoing off of the surrounding buildings. The only other sound was the distant roar of the traffic from a nearby motorway. The air was clear, and the sky above her twinkled with the light of a thousand stars. Steam rose from the open packet of chips that she was happily working her way through.

Rose sighed. It was in moments like this that she missed him the most. It was always in the little things - when she had Jaffa Cakes with her tea (he always did that), whenever she saw a banana, whenever she ate chips. They were all remainders of the bits they shared in - between all the running and saving the universe. The times when it was just the two of them, sitting around in the TARDIS kitchen, drinking tea and eating biscuits, regrouping after their latest escapee. Walking round in various branches of Tescos, arguing over which time period was the company's heyday (he swore it was in the early days with the local shop keeper, the personal element. She, on the other hand, loved the intergalactic era of the company), or adding yet another entry onto their Universal Blog, dedicated to the search for the Universe's best chip shop; they had quite the following, they'd even had a meet and greet once in a chippie on Oberon 5.

Even now, after all these years, she could still hear him. He would have been chattering away about something or the other whilst simultaneously stealing her chips (despite the fact that five minutes earlier he'd have insisted that he wasn't hungry). She would let him get away with swiping a few, before swatting him on the back of the hand and telling him to get his own. She would then have been on the receiving end of one of his puppy dog looks, against which she had no real defence. She would melt just a little inside and offer him her chips once more. Then he'd smile triumphantly, and continue eating what was supposed to be her dinner with gusto. No one stole her chips any more. Although she was, for all intents and purposes, reasonably content with the life she had carved for herself in this universe, she knew that she'd swap it all in a heartbeat to have one last adventure with the skinny alien who stole her chips, and more besides.

She was nearly home when she felt the pain explode in the back of her head - pain beyond any that she had never known. Mercifully she only felt it for a moment, before darkness consumed her.

It was a well-known fact that in the last twenty years, the British Empire had undergone a massive change, both socially and economically. The incident with Cybus Industries had taught the world and all its governments some hard, yet invaluable lessons - Britain, most of all.

One of the first things to be implemented was strict human rights legislation, and on the heels of this, a welfare system to help the most vulnerable of society. The Government was determined to make sure that no one could be taken advantage of for lack of food, heat or shelter again. This was paid for by the seizure of Cybus Industries and its patents by the Government. This move was felt by many to be an apt ending for the company.

Business dealings became transparent and became a matter of public record. Any scientific research that took place was subject to strict legislation, with regular government checks to ensure that all was as it should be.

The public also became more wary of technology, and with the public's aversion to the blue tooth headsets, the magazine industry soared. Jackie Tyler became a household name, and was the subject of many a column.

Communities bonded together in the wake of their mutual loss and devastation to help each other in their grief. Overall, things worked well. People prospered, and the gap between rich and poor gradually closed. They called it Britain's 'Golden Age'.

Inevitably, though, there were those who argued against the new order. Businessmen, scientists and political activists fought against the changes, and lobbied Parliament countless times to reverse them, to allow greater freedom for themselves and others affected. Parliament, however, was immovable, and all they had to do was to simply point to the countless memorials dedicated to the millions lost, and the lobbyists were instantly defeated. In the end though, as before, those who would not comply simply went underground, conducting their questionable dealings and research with even more questionable methods away from prying eyes. One such man was Professor Luke Rattigan.

A genius in his own right, he had graduated high school at fifteen, and had gone on to study medicine at Harvard Medical School, managing to fast track his course so that he qualified as a doctor by the age of twenty.

That was when he had met Professor John Sullan and SETI.

It was the day before his graduation when, at a meeting with his tutor, he had been introduced to the Professor. They offered him an exciting career with great prospects, learning things that no one would ever dream of. He had, naturally, jumped at the chance, and over the next ten years, been mentored by the Professor, eventually earning his Doctorate and becoming a recognized expert in the field of Xenobiology. Luke loved it - the joy of the unknown, the thrill of being the first to know. His job led him all over the United States, Mexico and Canada, working with SETI. It was after the debacle with Cybus Industries that he was first introduced to Torchwood in Britain and Europe, and it was there that he met Rose Tyler.

He had been working at the London Torchwood within their medical research division for a month before he had been introduced to her. He heard about her, of course, long before that. Stories of her exploits haunted the halls of Torchwood. She was their resident first contact expert, and apparently the stuff of legends. Upon hearing this, he had scoffed. He had seen her picture on the board in the staff room; she was barely out of adolescence. To him, she was just some little upstart of a girl - what did ishe/i know about anything?

It was at the end of his first week, as he stared out of the staff room window at the retreating spaceship, that he was forced to rethink his opinion of Rose Tyler and decided that she did, indeed, know a thing or two. In fact, he decided, she was entirely too clever - her knowledge of aliens was far beyond anything he had ever encountered before. She would have a plan worked out and put into action while everyone around her was still doing headless chicken impressions. She could name and figure out artefacts when all the others were stumped. In fact, the unknown bin in Archiving had (unofficially) been christened 'Rose's Bin'. For some unfathomable reason, it was pink.

It was on his official introduction tour by the Torchwood director Peter Tyler, (which, for one reason or another, was a month late) that he finally met the infamous Rose Tyler. He had been ushered into the lobby of Torchwood Towers, Mr Tyler introducing him to anyone unfortunate enough to cross their path, when Rose Tyler and her team walked through the door. Mr Tyler, spotting them, beckoned them over.

"And this is Alpha team. They're the best of the best, led by my lovely daughter, Rose. She's our first contact specialist," the Director announced proudly, gesturing towards one of the helmeted team members. "Rose, come and meet Professor Rattigan."

Recognizing the more infamous of the Tylers from her picture in the staff room, he watched as she approached; she looked even younger in person. Still, he held out his hand to her, "Miss Tyler. Nice to meet you," he said politely.

"Pleased to meet you too, Professor Rattigan." She moved her helmet to her other side to free up her hand. "Always nice to see a new face." She shook his hand.

He had always prided himself on his sense of touch, it was one of the reasons he had come as far as he had. His ability to discern the differences in the flesh, the subtle nuances in temperatures and textures from one being to another. This is what set him apart from the others in his field.

Her hand felt different to any human he'd ever encountered. For one, it was cooler, and there was no sign of perspiration, despite the fact that it was twenty degrees outside and she had been wearing heavy duty gloves up until a moment ago. The texture of the hand felt almost impervious, with nothing of the familiar graininess that he had come to associate with the human skin. In fact, it felt smooth, and oddly featureless. It felt alien.

Before he quite knew what had happened, Peter Tyler had bustled him off and introduced him to yet another person. Still reeling from the strangeness of her handshake, he was surprised he actually managed to say hello to them at all.

A few days later, he had still not managed to shake off the sensation of Rose Tyler's handshake. It had him gripped, and his mind was going round in circles trying to make sense of it all. So he did what all good academics did when confronted with a mystery; he researched. And what he found fuelled the fires of his compulsion even more.

Oh, there were records of her; school records, college and university results. Prior to 2002 and the Cybermen incident though, there was little or no detail to what he found. He even went so far as to ask some of her supposed former classmates about her, not one of them remembered her prior to 2002. It was as if she had just appeared here. He had also studied pictures of her from over the years. Apart from a few hairstyle changes, she had not aged a day. No procedure or product was that good; he should know. His wife had spent enough of his money on them and they had never worked for her. He decided to try one last test; he would shake her hand again.

It was a week later and a poor excuse regarding the origin of a piece of medical equipment that he had randomly picked up in the lab, that he finally managed to shake her hand again. It felt the same. He set to work. It took him a week to collate all the information he had acquired into a recognisable format and another week in order to go before his superiors at SETI in Roswell, New Mexico.

He leaned back against the wall of the deserted corridor, papers strewn around his feet where he had thrown them down in a fit of rage. His arguments had been rejected and crushed, not one of them was willing to see the truth, or the very present danger that was Rose Tyler.

Feeling a well of frustration and rage rise up within him, he kicked a nearby door. The resulting pain in his foot only served to distract him for a moment. He sighed, and, knowing that there was nothing he could do for the moment, he bent down and began to gather his papers. He didn't hear the footsteps as they came up behind him, and, jumped when a hand settled on his shoulder. He turned round, only to see his old mentor Professor John Sullen standing behind him. He stood up, facing him.

"Professor." He stuck out his hand. "It's so nice to see you again. How are you?"

The Professor grasped his hand. "Luke. I'm very well, but how many times must I tell you to call me John?"

Luke half shrugged. "Sorry, John. Old habits die hard. What brings you here?"

The Professor looked at him for a moment. "I heard about your meeting, Luke, and I know what they said. But I know you wouldn't have come this far without good reason, so let's go grab some coffee, and we can talk."

Luke, feeling a weight lift from his shoulders, nodded and followed the Professor as they walked out of the building together.

The Professor drove them out of the compound and onto the freeway, driving for quite some time until they came to an appropriately deserted truck stop. The Professor parked the car and led Luke into the small diner. Briefly stopping at the counter, he ordered two coffees and led Luke to one of the booths toward the back of the diner where they would not be disturbed.

Luke looked around him, observing his fellow occupants, he stuck out like a sore thumb dressed in his tailored suit. He pulled off his jacket and tie, rolled up the sleeves of his shirt and opened the top few buttons of his shirt, making himself feel mildly better. Thanking the waitress as she gave him his coffee, he grasped the mug and took a sip. He closed his eyes, letting the bitter flavour wash over his taste buds and sighed as the warmth filled his belly.

"They really don't make coffee like this in England." He said, opening his eyes and looking at the Professor, "It's all I can do not to spend all my money in Starbucks, even then though, it's still not the same."

The Professor rolled his mug in between his hands and chuckled, "I was in London last year; it was only a stopover flying back from Beijing, but you're right, the coffee was awful." He paused momentarily and took another sip from his cup, "But then again, I've heard some of the English guys back in the lab say that we can't make decent tea to save our lives. Do you remember Douglas Cook?"

"Didn't he work with you for on the collaboration project with UNIT for Project Indigo?"

The Professor nodded. "Yeah, he did, smart fellow. He transferred over to UNIT when our part of the research was completed. Anyway, every week the guy used to get care packages from his sister full of English teabags and something called Marmite. I tried it once, it tasted like something you would use to clean dishes with," he chuckled. "But we didn't come here to reflect on our cultural observations on our British cousins. Why don't you tell me what you've found?"

The Professor watched as Luke drained his cup and then seemed to shrink into the seat, tiredness and weariness evident on his features. He motioned over to the waitress for a refill. Luke smiled gratefully at him, he thanked the waitress and when she was back behind the counter, Luke spoke. "I wouldn't even know where to start," he sighed, resting his face against his hands.

"Why don't you tell me what sparked this whole thing off and we'll go from there?"

Luke sat back in his seat and took a sip from his cup and began to tell the Professor the story of Rose Tyler.

It was an hour later when he had finally finished his tale. The Professor was sat back in his seat, a contemplative look on his features as he observed Luke. Leaning forward in his seat, he spoke.

"Your story is an interesting one Luke, and, the fact that you have come this far -" he motioned toward the stack of papers that was now spread across the table, " -Collating evidence, setting up meetings with the management and even coming with me here. It's you at your best Luke, but what I want to know is; are you prepared to go just that one bit further?"

Luke screwed his face in puzzlement for a moment, "What do you mean?" He paused, and then slowly realisation spread over his features. He leaned away from the Professor with a horrified expression. "But that's...that's illegal, we can't do that!" He ran his hands through his hair, then leaned closer to the Professor, "If anyone even thought we were stepping outside the research legislation, we'd be imprisoned indefinitely. To actually go through with something like that." He paused, shaking his head. "If they caught us, they'd kill us. You saw what they did to Professor Van Raine." He hissed, his voice low so as not to draw attention to them.

"Luke, you know as well as I do that no one is going to act on what you've found. I mean, Rose Tyler; the darling of Torchwood, an alien? It's ridiculous." The Professor leant forward and grasped his hand. "Luke, there are ways in which we can go about what you proposed to the managers at SETI, and, I'm prepared to do this with you. But that'll mean going outside of their jurisdiction and you've got to decide if you're willing to take that risk."

Luke opened his mouth as if to reply, but the Professor held up his hand and continued. "Just… just think about it, because once we do this there will be no going back. Let's say no more about this for now. I'll drive you home, and you can let me know what you decide."

Luke could only nod, the magnitude of the thoughts running round his head proving too much for him at that moment. His head was so full that it was only as he put his key in the front door of his house that he even realised he had been driven home.

Luke spent the next week trying to process all that the Professor had put to him. Could he really do it? Could he really go that far? He spent hours going over and over the notes he had gathered, thinking out different scenarios in his head. He barely slept, tossing and turning as his mind refused to let him rest. His wife banished him to the spare room after the second night of disrupted sleep. Not that he minded; she snored like a Hippo with a sinus problem.

It was at the end of the week, as he went over his proposal for what seemed like the millionth time, that it hit him. He could do it; he had already made the step of going before his managers. He could take that next step without them. He had friends and resources and the Professor had agreed to help him. He picked up the phone and dialled.

The next few weeks passed in a blur, the Professor and he made plans and soon everything was set in place. It was as they set up the examination room in that the Professor asked Luke one last time; "Are you sure about this, Luke? We can always stop. You don't have to do this."

Luke looked at the Professor, studying him for a moment. He shook his head. "No, I'm sure, we can't stop now." The Professor's tight smile and a perfunctory nod was the only response he received. No more was said on the subject.

They followed her, marking out her movements and routine, trying to find the most opportune time. Whenever he saw her with her family, Luke ignored the feelings of nausea that would rise up in his stomach, clamping down on his emotions and focusing only on her alien-ness.

It was time. They were alone. Luke watched her as she walked down the street. He was almost disappointed that she didn't notice his presence, because then maybe he wouldn't have to do what he was about to do. He swallowed nervously and his hand shook as he released the safety on the handgun. Looking up, he took aim - and fired.