Head Notes: Sorry it has taken more than a week to get this one up. I added some scenes to go along with this story but for the most part I kept it pretty much the same. Mostly focusing and the Doctor and Clara's relationship. Enjoy!

Chapter twenty-one

Clara walked beside Missy in the sewers below the city. She didn't know why she still trusted her. She'd already hung her upside down and shoved her down a hole. She'd made it very clear that she had not changed from the murdering psychopath she was last year. There were a few moments she was tempted to just find her own way through the city. But every time she considered it, her mind went back to the Doctor alone in the Dalek city. No matter how much she wanted to, she knew she couldn't save him on her own. Until they could get into the city, she would have to put up with Missy's abuse for the Doctor's sake.

Suddenly she heard his voice. At first she thought it was just in her head until she saw Missy stop next to her. But it wasn't his usual haughty, overconfident voice. He sounded furious, hopeless, and desperate as he demanded that the Daleks bring her back.

At that moment she realized that he actually thought she was dead. With that realization, her mind flashed back to their conversation in New York. He had been so sure that something bad would happen to her that he had stopped traveling with her. And now after seeing her for the first time since then, that fear had been realized. Even though she knew it wasn't true, it still broke her heart to hear him like this. As she stood there in the dark, damp sewers, she resolved that she would get to the Doctor before he did something fatal. Because as long as he believed she was dead, he had nothing to lose.

XxXxXxXxX

The Doctor ran down the corridors as the old Daleks climbed up the pipes. Every cell in his body still stinging from the forced extraction. Regeneration energy was painful. It literally burned everything away during the actual process. It hurt even worse when it was siphoned out of his body like this. It was like his cells were on fire.

He stumbled as another jolt from the floor knocked him to his knees. He had to find Clara. Missy had managed to escape the Daleks so Clara must have as well. But where was she?

Hearing a noise, he looked down the hall to see a Dalek coming toward him.

"There's no point in lying to me," he warned the trigger-happy mini-tank. "Just tell me, where is Clara Oswald?"

"I AM A DALEK!" the Dalek replied.

"Yes, I know you're a Dalek," he said, wondering what being a Dalek had to do with Clara.

The defective creature continued repeating the same thing over and over. As it repeated the same words over and over an impossible idea began creeping into the back of his mind.

"Doctor!" Missy called, running up behind him. "Clara's dead. This is the Dalek that killed her."

He stared at her, hoping he had somehow misunderstood. He slowly turned his gaze onto the guilty Dalek as Missy described Clara's death, the rage building in his chest making his blood boil. He felt Missy press the Dalek gun into his hand. It was surprisingly light. At this the Dalek seemed to panic, backing away from him in terror. But no, he wasn't going to let it get away.

"Is Clara dead?" he demanded, brandishing the gun before the Dalek.

At first the Dalek simply repeated he same thing as before. Channeling his anger, he was preparing to fire the gun when the Dalek pleaded, "MERCY!"

The odd statement stopped him in his tracks.

"You shouldn't be able to say that," he breathed. Then he realized another odd thing about this Dalek. "Why aren't you trying to kill me?"

The Dalek seemed to be having a difficult time finding the right words. But of course in that machine it would. The only way the Dalek would be able to actually speak to him would be to open its case. Otherwise the case would keep censoring everything it was trying to say.

"Open your case," he ordered.

After a moment, the case began parting and the shell opened to reveal Clara's terrified, tear strained face. Her eyes were filled with fear. Fear toward him. At the moment, the horror of what he had been about to do burned into his memory, the gun weighing heavily in his grip. But he realized that Missy had known. She had ensured that it was in fact Clara before accusing her.

If Missy was still there when he turned around, he wasn't sure what he would do.

"Missy," he hissed furiously. "Run."

"Doctor," Clara whispered brokenly.

At that moment, his reservations broke down and he knelt down to her eye level, discarding the Dalek weapon on the floor. He disconnected the nodes from her temples and massaged the area with his fingers while apologizing to her. Just more proof that the Machine was right. He was a danger to those closest to him. He'd been so desperate to get her back that he had nearly killed her.

Behind him, Missy kept rambling on about something.

"I said run," he warned her.

He waited until her feet pattered away before looking back into Clara's eyes.

"I'm so sorry," he breathed. "I would understand if you didn't want to see me right now."

But Clara climbed out of the Dalek shell and pulled him into an unrelenting hug.

"Don't be ridiculous, you daft old man," she whispered.

He could feel her tears trickle onto his neck. After a moment, he returned her hug not quite understanding how she could just go from being held at gunpoint to embracing the very man that had done so.

"I don't understand," he started.

She pulled away to look into his eyes.

"Do you think I care for you so little?" she asked, her smile brightening behind her tears. His lips curled into a smile as he realized what she was saying.

Another jolt under the floor brought him back to his surroundings. The city was about to get sucked under the sewers by an advancing hoard of decaying Daleks. Grabbing the Dalek weapon, he grabbed Clara's hand and helped her up.

"We need to get out of here," he explained.

XxXxXxXxXxX

Clara flashed her eyes around the TARDIS. Even after all this time, it still amazed her that the Doctor was so brilliant and resourceful. And sonic sunglasses? She'd have never seen that coming.

"So Doctor," she called. "Where are we going now?"

For a moment the Doctor didn't speak. He looked up at her.

"Clara, believe me I don't want this any more than you do," he said sadly.

"What, send me back home?" she challenged. "Drop me off, like I'm a kid who's going to hurt myself on the swing set? You do that, Doctor, and I will not step out of this TARDIS."

"Clara, listen," he placated.

"No, you listen," she demanded. "I told you before, this is the life I want. I'm not a little kid. So stop treating me like one."

"Clara, you once told me that you had a duty of care for kids in your class," he explained. "Kids that weren't exactly completely dependent on adults. In fact, some of them were the complete opposite."

"Doctor, I just said, I'm not a kid,"

"Clara, I'm a Time Lord," he pointed out. "You're all children compared to me. Why can't you understand that? As a being that has had centuries of experience, this Earth and its people are under my duty of care. I have to protect you. Especially from me."

"Doctor," she said with a sudden curiosity. "How long has it been for you since you last saw me? And don't you dare lie to me."

He stared at the console.

"Twenty years," he finally answered.

"Twenty years?" she repeated. "Why, why would you do that? I've been kidnapped and tortured plenty of times before. What in the universe would be so different this time that you couldn't travel with me for twenty years?"

"Something was said," he stated shortly. "It gave me the impression that traveling with me would have consequences. Either fatal or….in other ways."

"Well, Doctor, they are human. They don't exactly know everything," she pointed out.

"She is not human," the Doctor clarified. "And she does know quite a bit more than they could ever know. And if she'd wanted to lie, she wouldn't have said that."

"Are you saying..?" she began.

"The Machine gave me a prophecy," he stated. "I don't know exactly what it means. But I know it is something to do with you. I didn't want anything to happen to you."

"So you made the choice for me," she realized.

"Clara, please, you still have a life ahead of you," he said. "You can still have a normal life."

"I don't want a normal life. And I certainly don't want you making choices for me," she said.

"Clara please, traveling with me is dangerous in more ways than one," he insisted. "And… I don't know what I would do if something happened to you. For your sake and mine, we have to stop."

"Fine," she agreed. "But it will be my choice. I will choose for myself when I stop traveling with you. But until that happens you will respect my choice. Deal?"

"Alright," he said after a moment.

"And before I forget," she took out a small stack of 3x5 cards. "These are for you."

He took them and thumbed through them a look of confusion on his face.

"What exactly are these supposed to be?" he wondered.

"I told you after New York that I would put together a project to help your bedside manners," she reminded him. "Except you never came back."

"Flash cards?" he repeated. "Isn't that a bit childish?"

"I actually find them very helpful," she said.

"So my entire dialogue is limited to 'I'm sorry. I understand that you all have names, and I will do my best to remember them?'" he read off one of the cards.

"Mostly they're a safety net, in case you are just a little too you and stick your foot in your mouth." She explained.

He set them aside in his pocket, shaking his head.

"Very well," he said. "So where do you want to go?"

"Somewhere there's a party," Clara answered.

"I know the perfect place for that," the Doctor said, throwing the gears into place.

XxXxXxXxX

The Doctor never stopped worrying about Clara. The Machine's prophecy playing in his mind with each additional adventure. It didn't help that there were dozens of close calls. Each one growing more and more dangerous and coming closer and closer to actually harming her. Sometimes he was able to convince her to let him handle the threat. But never without an argument. There were even times when he nearly lost all hope of her survival. That seemed to happen more often than not.

Every once in a while he tried to talk to her about his fears, but every time he did she implied that he was acting paranoid and overprotective. Maybe he was, he wasn't sure anymore. As time went on he stopped bringing it up, but his worry about her always remained a permanent fixture in the back of his mind. Right up until Trap Street. And everything went downhill from there.

XxXxXxXxX

The Doctor stepped into the TARDIS for the first time in billions of years. It seemed it had been at least half as long for the TARDIS. For a moment, the TARDIS looked dead. Not a light flickered in the darkness. But after a moment, life came into the TARDIS and the room brightened. He wasn't sure how the TARDIS ended up in the United States but at the moment he wasn't worried about that. He was more worried about finding this Clara that only existed outside his memory. He had to find her. He just knew that if he could see her face, he would have some memory of her.

There was a message on the chalk board. He wasn't sure if it was from Clara or something he had written years ago and had forgotten to erase. But for now he would keep it on the board. He closed the doors with a snap of his fingers and powered up the TARDIS.

XxXxXxXxX

End Notes: Not over yet. I am still working on the last chapter both as a coda to the series and an end to this story. I think it will be very sweet.