Note from Phoenix: This is my first try at Doctor Who, but it seems like a really fun world to play in! I'm NuWhovian scum and Matt Smith is my fav so I'll be playing with the 11th Doctor, but I found the TARDIS Wiki so I'll be adding in a *lot* of Classic Who.
As for where this fits in the seasons: end of season 7 but before season 8.
Also I will be switching POV between Rory and Amy within the chapters! I know this is 'bad form', but for this story and for this style it is going to work best for me.
Doctor Who: The Lemkin Factor
Rory woke on a cold metal floor with a powerful pounding in his head, the kind that made him believe he'd spent the previous night binge drinking down at the pub. Not a hundred percent sure that he hadn't done exactly that Rory experimented with opening his eyes. He was grateful that the lighting was dim. Still disoriented Rory turned his head to either side slowly to look around.
"Amy?" Rory whispered. "Amy?"
Amy's weak voice lead Rory to think that she was in a similar state to the one he was currently suffering from. Forcing himself to sit up he found Amy laying a few feet away. He crawled over to her and helped her sit up. She groaned pitifully and looked around in confusion. They were in a metal corridor of what looked to be an older spaceship of indeterminate origin.
"We have to find the Doctor." Amy said instantly.
"Yeah, right, also, I'm okay...how are you?" Rory asked in a hurt tone.
"Don't be like that." Amy shoved Rory's shoulder. "I know you're okay, Stupid, I can see you. But when I wake up on a spaceship with a blazing headache and the last thing I remember is being in bed on Earth, finding the Doctor becomes my 'first order of business'."
"You've got a point there." Rory admitted. "Last thing I remember is being on the TARDIS...we were going to a world made of crystal for some sort of festival."
"For a Crystal Festival it sucks."
"Yeah, I don't think we landed in the right place."
"We never do." Amy chuckled, instantly regretting it as her headache protested. "Come on, let's find the Doctor."
Rory wasn't sure how wandering aimlessly on a spaceship of unknown size was going to help them find the Doctor and yet every other time they'd tried something similar it had worked. As they worked their way through the maze of corridors they started to get a sense of how immense the craft really was. It was only years of space travel that told them they were under the influence of artificial gravity and not in the metal halls of an underground city on a planet. Nearly an hour of walking through the vacant corridors, chambers, catwalks, and decks they were no better off then when they started.
"Am I the only one who thinks it's unsettling that we haven't come across anyone?" Rory asked to break the silence. "Someone's got to be flying this thing, right?"
"It is frighteningly qui..."
Amy was cut off as bright white shimmering light appeared in the hall a few feet in front of them. When the light cleared the Doctor was there facing away from them. He looked around without looking behind himself before swearing under his breath and reaching over to the wall to type into the small console imbedded in it. The shimmering light reappeared over him.
"Doctor, wait!" Amy called out.
"Pon..." The Doctor said as he started to turn around. It was too late the transporter beam was already activated and the Doctor vanished.
"I suppose we should just wait here then." Rory said.
Amy just shook her head sadly. After waiting fifteen minutes the pair started to worry that the Doctor hadn't returned. Before they could seriously start talking about starting the search again they heard footsteps coming towards them from down the hall. Rory and Amy both breathed a sigh of relief when it was the Doctor who rounded the corner and not some angry alien life form. Although when Amy got a look at his expression she decided that he might well fit into the 'angry alien' category. She also noticed that his tweed jacket was buttoned up, something she couldn't ever remember seeing before.
"What happened to you?" Amy ask.
"Explanations later." The Doctor said briskly as he approached. "Let's go, Ponds."
Amy stopped with a surprised yelp as the Doctor snatched her wrist on the way past and nearly pulled her off her feet as he continued on down the hall with her in tow. Rory was quick to come along as well. Rory looked to Amy for an explanation to the Doctor's strange behaviour but all she could do is shrug. When they came to an intersection the Doctor didn't hesitate to turn to the left and then right at the next one.
"Where are we going?" Amy asked.
"Back to the TARDIS." The Doctor replied simply.
"Why not just 'beam' us there?" Rory suggested.
"The teleport on this ship is dreadful, barely works to get myself around, three might be a disastrous." The Doctor growled. "I hate teleport, particularly faulty poorly constructed teleport."
"Where is everyone?" Amy asked as the Doctor continued to pull her down the hall.
"I don't care." The Doctor snarled.
Amy looked back to Rory for help but this time it was his turn to shrug his shoulders as he walked quickly to keep up with them. Amy had never seen the Doctor in such a hurry when their wasn't an obvious immediate threat present. It gave her the feeling that there was an unobvious immediate threat present. She could feel his stress in the tight, almost painful, hold he had on her.
Unable to free her wrist from the Doctor's grip Amy had little choice than to follow along as he picked up speed. He wasn't exactly running, but he was certainly walking with a singular purpose in mind. Giving in to just following along Amy crashed into the Doctor when he came to a sudden dead stop. Rory didn't have any better success putting on the breaks and bumped into them as well.
Releasing Amy the Doctor took a few steps closer to the dark glass surface that was fixed to the wall. It looked like it was some form of control panel that would light up to the touch, but the Doctor wasn't interested in touching it. He was completely transfixed by his own reflection like a moth to a flame. Staring at himself he slowly reached up and ran the back of his hand across his jaw line as if to confirm that it truly was the shape he was looking at. Rory and Amy exchanged a concerned glances once more.
"Doctor?" Amy asked hesitantly.
"W...why do I look like that?" The Doctor asked himself more than Amy.
"Mostly because you won't get rid of the bow-tie." Amy replied. "A hair cut wouldn't hurt either."
"What?" The Doctor said as he was finally able to pull his eyes off his reflection. "No, I mean...never mind. We have to get out of here. Right now."
"We just got here...didn't we?" Rory asked. "I'm a little confused about what's happening, or happened."
"You have a gap in your memory, I'm sure we all do to some extent." The Doctor explained dismissively. "Don't worry about that."
"Oh, right, gap in my memory, no big deal, happens all the time." Rory said with an edge of panic. "Should I worry about where are we?"
"No. It's not the 'where' that concerns me so much as the 'when'." The Doctor said seriously as he looked at his wrist watch. "My watch is off by nearly five hundred years."
"How could you possibly know that?" Amy demanded.
"It's complicated. Just trust me."
"Doctor, what is going on?" Amy asked in a tone that was not to be ignored.
The Doctor had already started back off down the hallway. Rory had taken a step to follow him, but Amy stopped him. She crossed her arms over her chest and stood her ground in a way that showed in no uncertain terms that she wasn't going to take another step until she had some answers. Looking around nervously the Doctor gave in with a sigh and walked back over to the pair.
"There are some..." the Doctor searched for the right word "'hiccups' in my memory over the past twenty-four hours as well. However one thing that is crystal clear is that I remember regenerating, even though I should have just died, but never mind that, it is also why it's impossible that I still look the way you remember me looking. It doesn't make any sense, none of it does. I don't understa..."
"Wait," Amy interrupted "you 'should have just died'?"
"Regeneration is a tricky, and from the looks of things..."
Reaching up the Doctor unbuttoned his sport's jacket and held it open. Amy gasped in shock at the large duel bloodstains the Doctor had revealed. Rory instinctively stepped forward offer medical aid but the Doctor just smiled sadly and shook his head to let him know it wasn't needed. His shirt was soaked in blood high on his left chest and also lower on his right ribs with corresponding gashes in the fabric, one over each heart.
"...I was murdered."