The Doctor opened his eyes to find that they had actually ended up exactly where he'd wanted to go: the TARDIS sick bay. He looked over at River to see that the trip really hadn't been very hard on her. That was good. After all, he hadn't known what would happen.
Gently, he picked her up and laid her on a cot. The technology of the TARDIS was able to make the whole thing less painful, but there was still a little too much screaming for the Doctor's liking. However, before he knew it, their child was born.
River was breathing heavily. "Doctor, what is it?"
His eyes were wide, full of joy. "She's a beautiful baby girl." River smiled at this. She wouldn't have cared what gender it was, but secretly she had been hoping for a girl. "So what do you want to name her? What about Amelia or Jessica?"
But River had already thought it through. "Rain. Her name is Rain."
The Doctor was slightly confused. "Rain? How did you come up with that?"
"It just came to me a while ago. I thought it was perfect."
He just shrugged, as she was right: it was perfect. "Well, okay then. Welcome, Rain Song."
The Doctor could tell that River was tired, so he held Rain until she fell asleep, then placed her in his old cradle next to River. He was also exhausted from the events of the day, so he pulled up a chair and drifted off to sleep.
The Doctor was running, but he didn't know from what. All he knew was that he was sprinting through the TARDIS as fast as he could, doors flying past him. Finally, he ducked into one. The door he had chosen just happened to be a maze.
Oh, great! Why did I put this in here, again? Oh, right I thought it would be fun. Well right now, it certainly was not fun. Not only was he running for his life, but now whatever was chasing him could just pop out from around the corner, and he would never see it coming.
For a second, he thought about turning back and ditching his pursuer in the maze, but then he realized that he wasn't exactly sure from which way he had come. So now he was basically blind. He just kept running as fast as he could and hoping that he didn't turn the wrong corner.
As he ran past an intersection, he noticed a figure in the corner of his eye. At this, he began running faster. The figure had obviously seen him too, as it picked up speed as well. The Doctor took a left turn, then realized his mistake. This was a dead end.
However, he ran until he reached the end and then stood looking at the wall as if it would just move out of his way. He wasn't so lucky.
He heard the footsteps come to a stop behind him. Finally, he took a deep breath and turned around. The figure behind him was a tall, relatively young girl with brown curls and green eyes. She looked to be about eighteen. "Well, well, well. It seems I've finally cornered you."
"Who are you?"
The girl laughed. "I know it hasn't been that long, but I would still expect you to know who I am."
Then he looked into her eyes, and immediately he knew her. "Rain?"
At this, she became angry. "Don't call me that. Don't ever call me that! I'm not Rain anymore. My name is Lyra, Lyra Pond."
"No it isn't. Your name is Rain Song, and you can't change it," the Doctor shot back, without really thinking about the possible consequences.
"Oh, can't I? Well, I guess it doesn't matter. I wasn't exactly the one who came up with that name, anyway." She said this with a crooked grin on her face. As cruel as she was, the Doctor couldn't help but notice that she looked like River when she did that.
"Then who was?"
She began walking closer to him until she stood mere inches away. "The people who opened my eyes. The people who showed me what real life is. The people who told me the truth about you and all the damage you've done. The best thing that ever happened to me was being rescued by them."
By now the Doctor understood. Somehow, his daughter had been kidnapped by the Silence. Though he knew she was brainwashed, her words still tore through him like a knife. This was all too terrifying. He couldn't take it any longer.
The Doctor jolted awake. He instantly looked around to make sure that everyone was still there. Rain was still in the cradle, fast asleep. River, however, was gone. Panic shot through him, and he ran out the door to search for her.
"River! River, where are you? Please tell me you're here!" Frantically, he began to search all of her favorite rooms. At last he arrived at the last possible place she could be: the kitchen. He walked in to find her making tea by the sink. Relieved, he ran over and threw his arms around her. "River, I was scared to death! What are you doing out of bed?"
She was very confused at his reaction. "Well, Sweetie, I just came here to make some tea. And I don't need to stay in bed. Time Lords heal a lot quicker than humans, you know."
The Doctor tried to slow his rapid breathing. "Sorry, I just . . . had a sort of nightmare."
"Really? What about?" River knew better than to dismiss any of his dreams as fiction.
"It was about Rain. She had been kidnapped by the Silence, and they trained her the same way they trained you." At this, River's expression became pained. She hated thinking about her childhood. So much of it was impossible to remember, anyway. Then all of a sudden, her eyes grew wide.
"Doctor, there wouldn't happen to be any way for someone to break into the TARDIS, would there?"
He looked confused. "No, of course not. It's very secure."
"Then how did we get in here?"
"Well, I simply dialed in the coordinates to the sick bay using the vortex manipulator." He sounded very sure of himself.
"Yes, but if the TARDIS is very secure, then how was the vortex manipulator able to break in?"
The Doctor's eyes now grew wide, as well. "Oh."
At this moment, both of them took off running. River went to the console room to reinforce the security systems, and the Doctor ran to the sick bay. He ran in to find the cradle empty. Rain was gone.