Yeah, I probably won't ever tell you who the villain is...
By the way, about the Doctor dying/regenerating... I don't know. I have no idea what I'm doing. Truth be told, I'm not following anything, I'm just making this up as I go along, which you can probably tell.
Also, sorry about the wait, I've been busy, then I got grounded, then I got busy working on a sequel for My Daddy is a Time Lord (It's going to be called Lost in Time and Space, but it isn't up yet) and so yeah.

Oh, and Oochya (if that is correct) I never said that the Doctor was totally dead. And I never said he was alive. I didn't say anything...

Also- HetaPastaH3ro. No, we don't need to know what happened to the Ponds. All you do need to know is that Amy screwed up.

I'll give you what you been waiting for.

New!
I reposted this chapter because of a few errors.
(I can't spell)

The Ponds

"Doctor?!" Amy yelled, panicked. Carefully, she transversed around the field of broken glass until she was at the Time Lord's side. Rory and River both followed her, diligent to not cut themselves on the sharp edges. As River and Amy cleared the Doctor of broken glass, which had miraculously not cut anything important and only had embedded itself a few centimeters into his skin here and there, Rory checked the Doctor's pulse.

There was no movement at all under the nurse's fingertips.

"There's no pulse!" Rory told the others and Amy looked up, frightened. Before she could respond to him, the Doctor was suddenly engulfed in a bright light.

"Get back!" River said as she pulled the Ponds away from the Doctor just as the light turned to a point where it was blinding. As soon as it disappeared, the space where the Doctor had been was completely empty.

"What was that?!" Rory exclaimed. "He's gone!"

"Rory, look!" Amy said and Rory turned to face her. Her hands were glowing, just like before they arrived in this twisted palace. As the light from Amy's hand grew, both River's and Rory's started to light up as well. Before he had any time to react, the light turned blinding and then dimmed.

They were no longer in the large white room; they were back home where they had started.

The only difference from when they left was the fact that all four of them were covered in small cuts from glass.

"We're back..." Rory said in a state of disbelief. "Wha-How are we back?"

"Rory!" Amy yelled from the Doctor's side. "He doesn't have a pulse!"

The Doctor

The Doctor opened his eyes and sat up. The last thing he remembered was that he was basically choking on his own breath and suddenly everything's okay. Something had to be wrong; there was no way that this was real.

Standing up, the Doctor took a quick look around. It was a large room with the edges darkened so he couldn't see where it ended. The Doctor knew exactly where he was.

Back inside his head.

The Doctor looked around cautiously, waiting for the little girl to pop out and probably try to kill him again, and probably this time with a headache.

He sighed and rubbed his temples, where a headache had formed that wasn't too terrible. With a sudden wave of dizziness he stumbled back and there was a sudden whoosh of air and a pounding on his chest, right over each heart.

The Doctor groaned and wrapped his arms around his chest, but the assault continued and he doubled over. Falling to his knees, the Doctor looked up with blurry eyes. The little girl had appeared out of all too familiar black smoke and was walking calmly towards him.

"They're trying to save you." She said. The Doctor tried to get up but he fell back to his knees and she scoffed.

"Why are you doing this?" The Doctor asked, barely audible and out of breath. The girl's hair and clothes blew as another wind of fresh air came by.

"Do you remember? Do you remember me at all?" She asked. When the Doctor didn't answer back she sighed angrily. "What you did to me?"

"I remember that you deserved it." The Doctor said, groaning as the attack on his chest continued.

"And you don't deserve this?" She asked. "You do the same thing I did, but people die when you take them!"

The Doctor didn't respond back and he tried to get to his feet. The little girl could see what he was attempting to do and she walked over and kicked him in the side, right under his rib cage. The kick wasn't hard enough to hurt, but it was hard enough to send him down and cause black spots to dance in front of his eyes. The Doctor coughed weakly while the little girl began to pace.

"You see, to me, you're the monster. We take people from their homes, you and I. We both do it because we're lonely, and we need some entertainment. A pet, if you will. But there is one huge difference between us." The little girl paused in both her speech and her pacing to skip over to the Doctor and she knelt in front of him so that he could see in her dark, never ending eyes. "Do you know what that is, Doctor?"

The Doctor opened his mouth to reply, but as soon as he did black filled his vision. Suddenly he could feel everything; his back was on the floor, both his head and chest were hurting and his eyes were closed. Voices were washing over him and he couldn't pick out what any of them said, but one was being repeated several times. The english word for doctor.

The Doctor forced open his eyes but all he could see were blurry shapes. One shape, topped with a blurry redness that could only be Amy Pond's hair, gentle grabbed his face by the cheeks and said something to him. Before the Doctor even had the time to blink, he was gone, tumbling back into the black recesses of his mind.

Okay! I did this one in a bit of a rush because I didn't want to let you wait any longer. Sorry about that again...
But here it is! Please leave a review, tell me how I did, that sort of stuff and guess who the villain is! I dropped some clues in here, so look and see if they are good clues!