Amy & the Bad Wolf
Chapter 1
"Doctor, do you remember that room we were in when House took over the TARDIS?" Amy ask him. She figured that this was a delicate subject since he had never said anything about it at the time.
"Yes, I do Amy. And what is it that you want to know about that room? I told you it was a deleted room. That's all there is to it." The mysterious man went back to fiddling with a Rubix cube. He'd gotten several of them, and after failing to make it work he would toss it aside.
"Why did you delete the room, then? And who used it last?" The Doctor looked up at Amy and stared directly into her eyes. In her head she could hear him saying 'Rule one, The Doctor lies.' But something told her that this time he wouldn't.
"That was the old desktop for the TARDIS. That's what she looked like the day we met. But inside she was all broken and I had to repair her. So during the time that I was gone I spent that rewiring the mainframe and comparing color schemes and choosing out the glass floor. And that's why I deleted that room. New face, new TARDIS theme. Simple as that."
"Okay, well why did you have to change the desktop then?" Rory asked as he came over with a perfectly solved Rubix cube.
"How did you? But...but you're of average intelligence - no offense - but...rubbish they're broken they're all broken and somehow you can fix them."
"Doctor, back to the point." Amy snapped her fingers in front of his face. "Why was the TARDIS broken?"
The playful look on the Time Lord's face turned into one of the most depressing Amy and Rory had ever seen. They didn't mean to upset him, but there was just something in the back of their heads itching to know about that room ever since they had stepped foot in it.
"Because, it happened when I was regenerating. I...I didn't want to go." He said glumly. "The blast from my regeneration, as you've seen from when Mels regenerated into River can be quite powerful. It's a painful process and the emotion I felt before it happened was extreme. I blew up the TARDIS from the inside and sent it hurtling back towards Earth, where it landed in your backyard. It's a shame, if anyone I knew before came in here they'd be...they'd be slightly heartbroken."
"Doctor, what do you mean 'knew before?' How many others have traveled in the TARDIS with you? Are we not the first ones?"
"Amy, he's over 900 years old, you couldn't expect him to be alone for all that time." Rory reasoned, resting his hand on Amy's shoulder.
Tears were starting to form in Amy's eyes. Her entire body started shaking. "I thought I was special." She whispered as tears streamed down her face, glistening on her skin.
"Amelia Pond, you are special. Everyone I have ever traveled with is special. I don't let just anyone come with me, you know." The Doctor turned away from Amy's tears. He couldn't bear to see her cry.
Rory pulled her in for a hug and patted her head. No matter how much The Doctor hated seeing Amy cry, Rory would always hate it more. "Show us them. In the old room. Show us them." Rory said. "Is there any way that we can meet them?"
"Rory, you have to understand I've been travelling with humans for hundreds of years. There's no way you could possibly meet them all. Most of them...most aren't even alive anymore and even if I travel back into their timestream they won't know me. None of them would know me. It's just you two and River Song that have seen me in this regenerated form. Heh. Imagine that. The Eleventh Doctor who none of his old companions would recognize. At least when I was in my Tenth regeneration Sarah Jane and Captain Jack...Fine. We can go in the old room. But I can't promise you'll actually meet anyone."
Amy's eyes widened as she went into the somewhat familiar room. It looked so much different all lit up. The colors looked so different. She couldn't decide what she liked more. The bizarre shaped columns that surrounded the main TARDIS area were incredible. She ran her hands up and down the one nearest her. She felt a few bumps, but figured that it must have been from when the TARDIS was broken.
"This, is Martha Jones and Mickey Smith. Or I figured they'd be better known as The Smiths. Not the band, though. They fight aliens. I saved them from a Sontaran once. They're resilient. Martha, Martha helped me reverse a whole year that never should have happened. She's a brilliant girl." He paused while the screen switched.
"Ah, Captain Jack Harkness. He works for Torchwood, brilliant company now that he's in charge. They once put the world in very, very grave danger. But I suppose I'll cover that in a bit. Amy, are you paying attention?" The Doctor snapped at her, she was busy looking at the odd markings on the column she had been looking at.
"Yes, Doctor. Go on." She said. Half honestly paying attention.
"Alright, then this here is Donna Noble. Ah good old Donna. Another firey ginger, like you, Amy. Sadly things didn't end well with her and now she doesn't remember me. Any mention of me and she'll burn up. Of course that will only protect her, but oh never mind. She was a good lot of fun to have around."
"Doctor, what does this..." Amy started out. But then she was silenced as she saw the face of Rose Tyler.
"And this, this is Rose Tyler." The Doctor started. He was trying not to get choked up in front of the couple. "I bet she'd still recognize me. New face and all. She's...probably the most important girl -woman- I've ever met. She saved me from who I had become. A Destroyer of Worlds. Some would call me. I had just ended the Time War. Killing all of the Time Lords. Locking that point in time. I was a different man back then. And she changed me. Much as you've changed me, Amy. Except in her case I wasn't able to save her, like I did you." He wheeled around. "Amy, are you paying attention to any of this at all?"
"Doctor, that...that's the Bad Wolf." As soon as the words left Amy's mouth the TARDIS started jerking around violently. Amy grabbed on to Rory and clung to a column, while The Doctor was busy trying to find out what was going on. He kept flipping levers before he realized that he was in the wrong TARDIS. But then, it wasn't the wrong one anymore.
"Where...where are we, Doctor? Amy asked, uncovering her eyes. But The Doctor wasn't standing there. Instead there stood the Blonde he had called Rose Tyler along with a tall, skinny many with dark hair.
"Amy, Rory." Rose said. "Something's gone wrong wrong, and from the looks of it, The Eleventh Doctor is gone. We're here to help you. This is John Smith."
As the dark haired, tall man stepped forwards Amy gasped. "John Smith, but Doctor called himself John Smith one time...are you?"
"Amy, I think that that is The Doctor before you met him." Rory said, keeping on hand on his wife. He looked around and they were on a beach, and covered in sand. "Rose...where are we?" He asked.
"You're at Bad Wolf Bay. But don't worry we'll get you home. But for now, this is where things get complicated."