Hey gang, here's Chapter 4. I took a bit longer on this one because there's plenty to explain and I wanted to try not to sound too exposition-y.

I'd love to hear what people think of the story, so please R/R! It's always useful to know which bits people are enjoying, so I can more suitably write following chapters!

So Amy and the Doctor are both lost in this mysterious empty space ship, where strangers are there one moment and gone the next...

What would the Doctor do? It was with this question in mind that Amy had decided to navigate her way through the silent and empty ship towards the bridge. As far as she saw it, the bridge was where the people in charge would be, and the people in charge ought to know what was going on. Of course there was always the chance that the people in charge weren't very friendly, but that was something she would deal with later.

She was moving quickly across what she had now (thanks to the wall-map) defined as the cargo deck, the heavy metal doors between passages simply sliding open at her approach. It concerned her slightly that the first door she had come across had been so… ghostly. She had tried simply walking through the doors here and there that didn't automatically open, but they had been very much solid and no amount of leaning, pushing or kicking seemed to change the fact. It was another thing she decided to put out of her mind for the time being.

For now she had a simple plan: Get to the bridge, find someone in charge, establish what was going on, find the Doctor. She repeated the four stages over and over to herself like a mantra, murmuring it under her breath so as to remove at least some of the eerie silence she was surrounded by. The plan itself was perfectly simple, but it was hard to focus on when Amy was sure she could hear whispers around every corner, when the shadows seemed to move in the corner of her eye and when she felt so terribly alone.

The truth was that she felt like bursting into tears. Like curling up in a corner and waiting for someone to come and find her… for the Doctor to find her.

But she couldn't.

She was Amelia Pond, and she had waited for the Doctor for long enough. Now the time had come for her to find him.

She reached the end of a corridor where the door slid across to reveal a small, cubicle. Amy was hesitant. Something deep inside of her felt that it was a bad idea to step into such a small and confined space. She wasn't normally claustrophobic, but something about the tiny elevator ahead had her thoroughly unnerved. She glanced over her shoulder, a shiver running down her spine as she suddenly felt like she was being watched.

There was nothing behind her. The metal corridor stretched off around a bend, beyond her line of sight, and was completely empty. Amy tried to calm her already fast-beating heart. She might have even preferred to be faced with someone rather unpleasant now, than continue on completely alone.

In that moment she came to the new conclusion that she'd rather be in a small enclosed space with her back against a wall, than out in the middle of a deserted corridor, where anything could sneak up behind her.

She stepped cautiously into the small square space, and turned around to look down the corridor she had just been in, grateful for the wall she could now back up against. She looked at the set of buttons listed beside the doorway. All of them bore strange symbols that probably meant something to someone, but meant nothing to her. She sighed and pushed one at random.

The doors slid closed. Amy let out a long, scared sigh as she felt the elevator start to rise.

"Who are you?" said an angry voice suddenly, making her scream and leap back with fright.

She was no longer alone.

The door slid open suddenly and the Doctor fell through it, landing ungracefully on his back. He looked up.

There was no one else around - no one to have set off the door besides him… He rolled over and leapt to his feet, pointing his screwdriver at the doorway.

"Motion sensor…" He muttered to himself. "So why didn't you activate before now?"

He only pondered this for a moment before setting off down the corridor.

It was a woman. She was dressed in plain, light blue scrubs, though Amy suspected not for medical purposes. The woman was filthy, her clothes torn in places and worn out at the knees, and she looked thin and gaunt like she hadn't eaten in some time. Her stare was wide and intense, her expression urgent as she demanded once again for Amy's identity.

Amy could barely breath, let alone form an answer, and she clung to the wall for support as she waited for her heart to stop racing. The woman slowly stepped forwards and gently prodded Amy on the shoulder. After a moment's pause, she stepped back again, then leaned over to the list of buttons and pushed one at the very bottom. Amy felt the elevator come to a sudden stop.

"Where did you come from?" the woman asked, more softly. She seemed to have realised how much she had frightened Amy with her abrupt appearance.

"I- I came with a friend," Amy stammered eventually, when her pulse had returned to a more normal pace. "We came by accident in a …ship."

The woman sighed, leaning against the opposite wall. "And then your friend disappeared?" she ventured.

Amy frowned, and nodded slowly.

"I'm sorry," the woman said. "You shouldn't have come here."

"Who are you?" Amy asked, "What's happening here?"

"My name is Andrea," the woman replied. "I was a research assistant here. Who are you?"

"Amy."

There was a brief, awkward silence following these introductions.

"What is this place?" Amy asked eventually.

"It was a mobile research lab," Andrea sighed. "Now it's a ghost-ship."

"Ghost-ship?" Amy repeated uncertainly, feeling her heart speed up yet again.

Andrea nodded darkly. "We were conducting experiments," she explained. "Experiments ruled too risky to be formed back on Earth. So we were sent out here where we would do no harm should it go wrong…" her eyes seemed to lose focus as she spoke, like she was no longer seeing Amy and the elevator, but gazing out into the distance, remembering everything from her story.

"… And it went wrong?" Amy finished.

Andrea nodded once again. "We're safe in here," she said suddenly, gesturing to the elevator. "The lift system is lined with a sealant that the frequencies can't penetrate. But as soon as you're out there…" She trailed off again. "Have you ever seen a ghost?"

Amy shook her head. "Not recently," she replied, trying to ignore the nagging feeling that she was trapped in a lift with a lunatic.

"Well leading theorists have posed the thought that ghosts aren't really spirits of dead humans, but rather alien beings that simply live on a different physical plain from us," Andrea explained hurriedly, with a tone that suggested she had summarised this concept many times before. "A different plain is really just a place where living forms resonate at a different frequency. A different frequency of vibration. If something moves fast enough then the human eye can no longer see it. What we were sent out here to find out, was if we could change a resonation, so as to make contact with these beings on the other plains."

Amy blinked. It was like the sorts of things the Doctor spoke about, but somehow he made it all sound far less…. Scary.

"So you were trying to turn people into ghosts?" she asked, screwing her face up in semi-confusion.

"Not exactly, just… transport living things between the different frequency plains. They built a machine to do it. To alter the resonation of a living being. They brought the machine out here, pointed it at the test subject, and turned it on."

Andrea's expression became distant once again as she spoke. "It was so quiet, so… instant. Everyone just vanished."

"Where did they go?"

"To different plains," Andrea shrugged. "The machine didn't just affect the single test subject, but the whole ship. A thousand people suddenly separated into different resonating frequencies. We can't see each other, hear each other or touch each other. And the machine seems to be running through a cycle, changing the frequencies every few minutes, so one moment you're there, then you're half there and half not, and then you're gone completely."

"Well, that would explain why I fell through a closed door," Amy sighed, trying to digest all the information.

"It's only living things affected, which is why the ship stays the same," Andrea went on. "Sometimes you're resonating fast enough to pass through walls, and other times you can touch things just as normal."

"I saw a man," Amy said suddenly. "He was running, and he grabbed my arm, and then he vanished."

"You crossed frequencies with someone," said Andrea. "The machine set you on the same plain as someone who happened to be nearby. It happens, infrequently, and in most cases when two people do resonate the same, they're never in the same room. It's what's happening now in fact, though that's because we're sealed in this elevator. It's the reason we've not already shifted into different frequencies. The second I open that door again the odds of us ever happening to meet again are… astronomical. I only managed to get in here at the same time because I saw the lift door open and figured someone on a different plain was heading in here. We synced frequencies as soon as the door shut."

Amy wasn't really listening anymore. She felt the bottom of her stomach drop, and her whole world grow dark and cold. The odds were astronomical? Unlikely to ever meet again? The Doctor's face flashed into her mind. She thought back to that brief moment before they had stepped through the TARDIS' doors. Those few precious minutes they had together before…

Would she never see him again?

"There are over a thousand people here," Andrea murmured, "And every single one of them is walking alone, around a silent and deserted ship."

Amy felt sick. The thought of never standing beside him again, never feeling his warm embrace at the close of another adventure, never seeing the deep and endless world in his eyes…

"No," She whispered.

"No?"

"No," she repeated, looking up fiercely, her eyes brimming with tears and burning with determination. "This can't be right. This can't be…it. I can't just give up and stay here alone…"

"Well what are you going to do?" Andrea scoffed. "There's no chance of getting away. The first wave of panicked idiots must have already launched themselves off in the escape pods, because there are none left."

"Why doesn't someone just turn the machine off?" Amy asked, trying to blink the tears out of her eyes.

Andrea sighed, "If I knew how then I'd do it myself. It's a complex piece of technology… I have no idea how it works. The operators obviously haven't done it, which means they're either part of the number of people who jettisoned themselves to safety or…"

Amy frowned as Andrea's eyes grew wide and fearful.

"Or what?" she asked. "What do you think happened to them?"

"Remember I said we were investigating the possibility of aliens on the other plains?" said Andrea, her voice trembling and barely more than a whisper.

Amy nodded slowly.

"Well," said Andrea, "We found some."

The Doctor was used to being alone. It was something he had endured time and time again, and even with company he generally felt somewhat detached or separate. He tried to make sure he had people around him to prevent him from simply getting lost inside his own thoughts, something easily achieved with a mind as vast as his.

Feeling alone though, was just a natural state of being for him. The last of his kind, always the smartest in the room, always the one with the responsibility to keep everyone safe, always the leader and even in a room full of people, always alone.

But he never felt lonely.

Feeling lonely was different to just knowing you were alone, because you were the only one like you. Nobody could ever get close, because no one could ever understand. The Doctor had felt completely alone in all of time and space since the Master died. He was the only one of his kind. The last. It was a lonely path to walk by its very definition.

But here, somehow, walking through the empty corridor of a strange, desolate space craft… The Doctor felt lonely.

His normal fearless, confident, curious nature usually allowed him to march through any bad situation regardless of the side-factors, or the dangers. If there was an end goal of fixing some sort of problem, saving some sort of victim or even running from some sort of monster, generally he could carry on alone. It didn't bother him.

But this was different. There was an emptiness inside that he'd never felt before. There was something missing.

There were occasions in the past when he'd almost lost the TARDIS, and the thought had made him feel sick and dizzy, like a part of him had died.

This was so much worse.

He hadn't really explored enough yet to make any form of real conclusion about where he was, or what had happened to the TARDIS… But he was beginning to understand his own thoughts well enough to know that neither point was very important to him right now.

Right now the thing that was missing, was something he hadn't even realised how much he needed. How much he had grown to depend on. How much he cared for.

Oh how he hoped she was ok.