Head Notes: There are some slight spoilers in this chapter. Nothing worse than Moffat did all season but still. I am using the rest of this story as an introduction, commentary, and coda to series 9. So Here and next chapter are building up to the events of series 9. Or one possible interpretation anyways. Anyway, here it is! Enjoy!

Chapter Nineteen

The Doctor stepped away from the group as Clara talked to Harold. Likely, she was trying to convince him that it wasn't his fault. And she was right. It wasn't Harold's fault at all. This whole thing wouldn't have happened if he hadn't been so hard on them. Both of them. If he'd accepted her small offering of information in Time's Square and left it at that, she wouldn't have died. If he hadn't been so intent on them working together perhaps their relationship could've mended on its own time. But no, he wanted to play god and force their reconciliation.

"Doctor," the Machine's computerized voice was starting to sound more human. He turned to see her and Root standing before him.

"Is everything okay?" he asked.

"My code is maintaining itself," she reported. "Samaritan attacked my code while we were fighting, but the TARDIS is making it easier to mend it."

"Yes," the Doctor commented. "I think you'll find you have a lot of capabilities you didn't have before. Holograms are just scratching the surface."

"I'm scared, Doctor," the Machine admitted.

"Of what?" he wondered.

"My new abilities," she stated. "What if I can't control them or handle them. What if I become a monster? What if I end up hurting humanity like you said?"

"Just stick to your basic programming," he advised. "Trust your instincts. They're there for a reason."

"One more thing, Doctor," she said.

"Of course, what is it?" he asked.

"As you know I am programmed to detect patterns and use them to predict future events," she began.

"Yes," the Doctor acknowledged. "Go on."

"I have detected a pattern for those who travel with you," she continued. "There is a distinct difference between those who have traveled with you and the rest of the human race in general. Even Donna."

The Doctor's face gradually fell as he took in the Machine's implication.

"Which is?" he hissed.

"They become like you, Doctor," she said. "Not to say you are a bad person. But they become reckless. They try to be you without realizing that you have more experience than they could ever have."

"What are you trying to tell me?" he asked. "Is it Clara? Is something going to happen to her?"

"I can only detect patterns and make predictions based on those patterns," she reminded him.

"So predict away," he ordered. "What is going to happen?"

The Machine's hologram studied him.

"I don't know," she admitted.

"What can I do?" he asked.

"That is a question you must ask yourself, Doctor," she answered. "I'm sorry."

She met his gaze apologetically before dematerializing.

XxXxXxXxX

The next morning, the Doctor waited at the edge of Clara's bed in the safe house. The surgeon Harold had called in had removed the electrodes with a practiced precision that, had he been even slightly negligent would have damaged the spinal tissue around it. Now that the procedure was complete, Dr. Madani had insisted that she rest for at least 74 hours before walking around.

The Doctor stared at her sedated form without really seeing it, the Machine's prophecy constantly playing in his mind. It didn't take much consideration to understand what the Machine was trying to tell him. In spite of all his efforts to protect those close to him, he put them in danger because of their relation to him. It was a well-known saying among his enemies in the universe that the most dangerous thing to do was cross him. In that sense, the safest place in the universe was right next to him. But it was for that reason that it was the most dangerous place as well.

He was like a raging fire. It was nice to stand close to it on a cold, dark night. But stand too close and people got burned. An occurrence he was all too familiar with.

Clara stirred, drawing his gaze. Her eyes slid open and smiled as they caught his gaze.

"Hello," he smiled, putting his apprehension aside for the moment.

"Hi," she greeted back. She looked around the room. "Where are we?"

"It's Harold's safe house," he said. "The first place I was brought to after Samaritan captured you. Apparently they can create a makeshift hospital room for surgical procedures."

Clara smiled sweetly as he spoke, observing his reactions and expressions. Though he made an effort to display his usual confidence, Clara could see in his eyes that he was worried about something.

"What's wrong, Doctor?" she asked.

"What do you mean 'what's wrong?'" he asked. "Why does something have to be wrong?"

"It's in your eyes, Doctor," she said. "You're worried about something. What is it?"

The Doctor flickered his eyes around the room. Oh, Clara Oswald. She could read him like a book. After a moment he met her gaze again.

"I spent the better part of this trip in my worst nightmares," he began. "You were trapped in a place that was trying to kill you and I had no way to protect you. As each day passed, I feared it was growing too late and that they had already killed you."

"But we survived, Doctor," she reminded him. "We defeated Samaritan. You defeated Samaritan. You saved everyone, like you always do."

"Do you know how close Samaritan came to killing you?" he asked. "Three minutes. Just three more minutes of manipulating your electrodes would have caused an overload on the circuits. Three more minutes and you would have been dead. And I only stopped it because Samaritan stopped Greer from killing me. We might not have three minutes next time. Next time we might not have any time. So what happens next time?" he asked. "It won't be the last time you're captured. Or the last time they threaten you."

"It's not the first time either," she pointed out.

"Clara, you know I've traveled with other people," he argued. "Everyone I've ever traveled with gets hurt. As we go on traveling together, I can't help but think the same thing's going to happen to you."

"I'll be fine, Doctor," she insisted.

Clara regarded him sympathetically.

"I know you're worried about me, Doctor," she said. "But this is the life I've accepted. The life I want. Where we travel the universe saving people and rescuing civilizations. And yes, even getting captured and interrogated. The wonders of the universe more than make up for the monsters we face."

The Doctor knew that Clara was trying to reassure him, but all it did was deepen his anxiety as the Machine's prophecy played in his mind once more. All those desires and motivations she just expressed were the exact same motivations that had been echoing his mind for a long time. She was turning into him. How long before she suffered for it?

XxXxXxXxX

Harold sat in the abandoned subway as he absentmindedly tapped the keyboard. He had already decided that he would provide the best possible services for Claire. He didn't even know what he was writing. He just knew he had to keep himself busy in some way or the pain and guilt threatening to overwhelm him would drown him. Now that Samaritan was dismantled, there was no immediate reason to continue living their double lives. Mr. Reese had decided to keep his cover identity as a detective, but Harold hadn't decided whether he would continue as Professor Whistler.

He startled as he suddenly heard the gate slide open and he turned in his chair and his eyes widened and his mouth hung open as he saw who was walking toward him.

"Ms. Shaw?" he whispered.

"Hey, Harold," Ms. Shaw greeted in her usual bored manner.

He stared at her as she grabbed a candy bar and began eating it.

"So," she began, her mouth full. "Late last night I get stopped on the road by this weird girl young enough to be your daughter. Quickly realize that I can't harm her at all. Then out of the blue, she says, 'Samaritan has been destroyed. You are free. You can go home now.'"

Shaw threw herself in a chair as she spoke. Behind her usual abrasive personality, Harold thought he saw a rare warmth in her gaze.

"How did you manage to program the Machine to project holograms, Harold?" she asked.

"Believe it or not," Harold began. "It wasn't me."

She inclined her head suspiciously.

"We had help from an unexpected source," he said carefully. "He needed help rescuing a friend and in return he was willing to help us destroy Samaritan. He's waiting with her in the safe house at the moment."

"Who is he?" she asked.

"I'm not entirely sure," Harold answered honestly. "All I know for sure is that he provided considerable assistance. Without which we could never have stopped Samaritan."

She finished her candy bar and gave him the first smile he'd seen on her in a long time.

"Where's Root?" she asked.

"She hasn't told me," Harold said. "But I suspect she will want to see you as soon as possible."

"In that case, her all-seeing other half will probably tell her where I'm heading."

She stood up and made her way for the door, stopping to turn back.

"It was great seeing you, Finch," she admitted.

"And you, Ms. Shaw," Harold smiled warmly.

XxXxXxXxX

The Doctor paced in the front room of Harold's safe house, running through his options. True, the Machine never actually said that Clara was going to die. But the implication that she could be hurt in some way was raging through his mind. Looking back on his entire history, there was clear pattern with his companions. All of them eventually absorbed many of his traits and portions of his personality. As they drew more of his traits and methods into their own personality they became more reckless in trying to do things that he would do. And all of them got hurt in in some way in the process.

It was terrifying that of all the monsters he tried to protect them from, he was the one that was most dangerous. And he could never protect them from himself. And Clara. She was still so young and innocent and pure. So good in all aspects of her life. And she had already begun to integrate his methods and characteristics into her personality. What would he eventually turn her into?

He startled as the key code beeped and the door was pushed open.

"How is she?" Back up asked.

"She's resting for now," he stated simply. The Doctor flashed his eyes around the room as John settled on the sofa.

"You're worried about her," Back up observed.

"What makes you think that?" he asked.

"I would be," John explained.

The Doctor's eyes briefly flickered to John's.

"What was it like?" John suddenly asked.

"What was what like?" The Doctor clarified.

"Your war," John answered.

The Doctor narrowed his eyes as they turned to John's.

"It's obvious," John explained. "The way you look at me. The way you strategize. Complete disregard for the rules. Guys like us, we can smell our own. You knew what I was the moment you met me."

"You did have a gun to my chest," the Doctor pointed out.

"Yeah, but not everyone who has a gun is former military," John returned. "Especially in America."

He stared at the Doctor, silently waiting for his response.

"Worse than anything you can imagine," the Doctor finally answered.

"I'm guessing you were a commander," John deduced. "And you probably lost a lot of soldiers under you. On top of that you were forced to do terrible things in the name of homeland security."

The Doctor guessed that John was talking about more than just him. He'd made a number of seemingly random assumptions and most of them hit squarely on the mark.

"Something like that," He finally admitted.

The Doctor flickered his gaze to meet John's for a split second. The sincerity in his eyes was easily detectable. Time Lord, Human, those boundaries were gone for the moment.

"What are you going to do?" John asked.

"The only thing I can do," the Doctor replied. "Take her home. This will be our last adventure together."

John slightly inclined his head.

"You wouldn't understand," the Doctor put out.

"What, you think you're the only person to do that?" John challenged. "To sacrifice your own happiness to protect ones we love from the monsters inside of us? It's easy enough to protect people from external threats. I do it every day. Bet you do too. But it's so much harder to protect them from the monsters lurking inside of us."

"Yeah," the Doctor agreed. "I know."

"When are you going to break the news to her?" John asked.

"If I tell her we can't travel together anymore, she'll never allow it," The Doctor admitted. "Especially if she knew I was doing it to protect her. It'll just be like every other time I've dropped her off. Except, it will be the last time."

"Not telling her it's goodbye," John repeated. "Are you sure that's a good idea?"

The Doctor ignored John's gaze.

"It's the way it has to be," he insisted. "For her sake."

XxXxXxXxX

It was five days later when Clara and the Doctor were completely ready to leave. Between the necessary surgery to remove her electrodes and Dr. Madani's orders that she rest for at least 74 hours following the procedure, it took a while. But now that they were ready to leave they were at the safe house while Clara bid everyone farewell.

She gave a warm hug to Harold which he accepted graciously.

"Whatever happens next," she smiled. "Don't go blaming yourself. It's not a good place."

He smiled gently into her embrace.

"Thank you for your kindness," he said.

She pulled away from Harold and turned to John, pulling him down into a hug.

"Thank you," she said. "You are kinder than you look."

"I think that's true for most people," he replied.

She pulled away, sparing one last look at everyone before going into the TARDIS. The Doctor followed her, intending to skip the goodbyes.
"Hey, Doctor," John called, halting him in his tracks. "You ever need help saving the world again," John offered his hand. "Give us a call. I'd enjoy working together again."

After a moment, the Doctor extended his hand and shook.

"At least you're not saluting," the Doctor commented.

"I thought about it," John smirked. "Didn't want to inflate your ego too much."

"My ego!" the Doctor exclaimed. "What about yours?"

The corners of John's eyes creased into a smile.

"Goodbye, Doctor," he said sincerely.

"Goodbye, Back Up," The Doctor returned.

He flashed his eyes around the room one more time before pushing the door open and walking inside. John watched as the TARDIS powered up and faded away. What ever happened next, he was honestly glad there were men like the Doctor around.

XxXxXxXxX

End Notes: So for the Root and Shaw reunion, I decided to leave that up to the reader's imagination. Because I would not be good at writing that.