"What happened?" The Doctor asked groggily and tried to withhold the panic at the feeling of déjà vu that washed over him. Emma's head appeared over him and all the anxiety rushed out of him all in one go.

"I don't know. I couldn't really see," Emma said as he sat up and rubbed the back of his head where the pain was radiating from.

"I'm surprised you didn't go after them," he said. Emma shrugged.

"I thought you would worry if you woke up and I wasn't here," she said. The Doctor sent her a confused look. He'd been expecting a sarcastic comeback and the fact that Emma hadn't said one was mildly concerning.

"Are you okay?" He asked as his confused look morphed into a concerned frown and Emma blinked in shock.

"Me? Why wouldn't I be alright?" She asked and that still wasn't the sarcasm that he was expecting.

"You didn't give me any cheek," he said.

"Oh, sorry were you missing it?" Emma asked with an eyebrow quirk and some of the worry loosened from his chest.

"Well yes why else would I have asked about it?" He teased and flashed Emma a smile which she returned hesitantly. All of the worry that had disappeared came racing back, stronger and fiercer than it was before. His tongue felt like lead as it continued to move. "We should go back to the TARDIS."

"If you think that's best," Emma said, and his hands came up immediately without conscious thought to cradle her head in his hands while his fingers skirted over her scalp looking for some indication of a head injury.

"I do think that's best," he said distantly as he pulled his hands away and stood up from the floor. Her curls hadn't felt quite right against his fingers, but in a way that he couldn't explain with any kind of logic, they had felt a little too manicured under his fingertips. Emma shrugged which made his worry ratchet higher.

As they walked, he kept a careful eye on Emma, not that keeping an eye on Emma was unusual, but the amount of detail he was taking in was.

Nothing about this situation made sense. Emma wasn't being her usual snarky self, which would have caused enough worry, but on top of that she wasn't displaying the physical tells of nerves or panic that she would have shown if she were worried enough about him to not be snarky.

He noticed hundreds, maybe thousands of tiny inconsequential things that are wrong on the walk back; her fingers weren't twitching, she wasn't fiddling with her hair, the list just kept growing along with his horror.

When they enter the TARDIS, he is suddenly reminded of Donna, how much it had hurt to walk into the console room after her while knowing what he had to do. He took a breath and crossed his arms in front of himself protectively. There aren't very many things that could offer an explanation for what was currently going on and he while he's pretty sure he knows which explanation it is, he also knows that this is going to hurt him for a long time to come.

"How old were you when we met?" The Doctor asked roughly. Emma laughed awkwardly and looked at him like he was crazy, but the expression was just a little bit off.

"Twenty." And with that the Doctor knew absolutely one hundred percent that the Emma standing in front of him wasn't the real one. Even beyond the fact that this clone had given him a wrong answer, the real Emma would have had to clarify which first meeting he was talking about. His eyes fell to the fake Emma's neck and that shredded any doubt that could have lingered.

"Where is your key?" He asked and the fake Emma blinked at him in shock as she reached up to her bare neck.

"I must have left it in our room," she said, and the Doctor shook his head slowly.

"You've never taken it off. Not since the day I gave it to you." He took a few steps forward as he pulled out his sonic which the clone eyed nervously.

"Doctor what are you doing?" the clone asked, and the Doctor swallowed.

"Emma, if you can hear me, I love you and I'm coming to get you." The clone's eyes widened in fear and the Doctor squeezed his eyes shut as he soniced it and didn't open his eyes again until he heard the shell hit the floor. The Doctor did not have the strength to watch an exact replica of Emma fall lifelessly before his eyes, even if it was a necessary evil. He stepped over the shell carefully and started the TARDIS.

"I need you to come with me and not ask questions for a few minutes," the Doctor said as he threw the doors open in front of Jack, who blinked at him in surprise before he nodded and stepped into the TARDIS.

"Doctor is that Emma on the floor?" Jack asked and the Doctor sent him a look as he started the TARDIS again.

"I said no questions," he said as he stormed towards the door again and opened it to usher Mickey and Martha in. They gave Jack a questioning glance, but he just shrugged as the Doctor flung a few levers on the console.

"Doctor?" Sarah asked as he stepped out in her attic and everyone followed after him.

"I need your help," he said. Sarah studied him carefully before nodding.

"Of course, but what with?"

"Emma's been kidnapped," he said.

"But she was in the TARDIS?" Mickey said and gestured backwards.

"It was a clone of her, obviously made to make me think that Emma wasn't missing so that I wouldn't go after her, so they had time to build the child," the Doctor explained a bit more harshly than intended. His heart lurched as he realized that if Emma were here, she'd elbow him and gently chastise him for being rude. It certainly hasn't taken him very long to start missing her desperately. He suddenly understood Eleven a lot more.

"Child?!" Martha and Jack said incredulously at the same time.

"Clone?!" Mickey repeated.

"Who's they?" Sarah asked and the Doctor swallowed down his rising anger. After Markus's scared pronouncement that someone wanted Emma for something bad, he'd kept tabs on certain groups and people, something he hadn't told Emma about. There had always been one group on the top of the list, no matter the scenario.

"The Papal Mainframe. They've always wanted to have the power and influence of a god and what better way than a half human, half Time Lord raised in their doctrine." He paused and tilted his head. "They also don't like me very much."

"So is Emma pregnant?" Martha asked and the Doctor shook his head.

"No. I would know if she was." Martha gave him a frustrated look.

"But that's how humans make babies Doctor," Martha snapped like she needed to spell it out for him. He looked up at her, but Sarah beat him to the answer.

"But Time Lords genetically engineered their children," Sarah said. Jack suddenly got a minorly horrified expression on his face.

"You don't think that they got Madam Kovarian to help them, do you?" He asked and the Doctor clenched his jaw and nodded sharply.

"She's the only one with enough skill and sadism to try," the Doctor said.

"Who's Madam Kovarian?" Martha asked.

"Imagine a genetic engineer who completely obliterated any idea of ethics. That's Madam Kovarian. She made creations so horrifying that the Sontarans turned and ran," Jack said. A heavy silence fell over the attic as everyone processed that.

"Why would they take Emma though?" Mickey asked and the Doctor looked up at him. "Everything makes sense to me except that."

"She can speed up the process. If they can make her believe that it's real, then she can make it real more or less. Which they need because I realized that they left me with a clone in less than half an hour," the Doctor said and clenched his hand into a fist. He was trying so hard to not get angrier than he already was because he needed to be able to think.

"But how do you know that it's them?" Martha asked.

"Because there was a little boy who could see into the future who said that someone wanted Emma for something bad. So I kept my eyes and ears open for trickles of rumours and they are the only ones who are close." His words came out as almost a scrape against his throat. He'd been on the lookout to prevent this from happening. And he'd failed.

"So how do we find her?" Jack asked. The Doctor turned to look at Sarah.

"That's why we came here. I need Mister Smith to look for this wavelength." He held out a scrap of paper for Sarah which she took and stepped towards Mister Smith who opened with his usual grandiousness. "It's her key."

"TARDIS keys give off a particular wavelength?" Martha asked.

"Usually no, but I made Emma's special so that I could always find her. Anywhere, any when." He gave the group a slightly sheepish look as Jack raised his eyebrows up at him. "I'm sure the Papal Mainframe will be trying to block the TARDIS so I can't find her that way."

"If they block the TARDIS how are we going to get her?" Mickey asked and the Doctor laughed darkly.

"The Papal Mainframe never considered the fact that the TARDIS loves Emma just as much as I do. I'd like to see them try and keep the two of us away from her." Martha shifted uncomfortably at his words and he realized that Martha had never really seen him as a solider, despite the fact that he had managed to turn her into one briefly.

"Doctor I have located the origin of the wavelength," Mister Smith said, and the Doctor stepped towards the display screen.

"Demon's Run," he said.

"What like that old poem?" Jack asked and the Doctor spun to face him with a frown of confusion on his face.

"What poem?" He asked.

"Demons run when a good man goes to war. Night will fall and drown the sun, when a good man goes to war. Friendship dies and true love lies, night will fall, and the dark will rise, when a good man goes to war," Jack quoted after he paused a few times in his recitation as he made sure that he was remembering correctly.

"What does that mean?" Mickey asked and the Doctor sighed and rubbed a hand over his face.

"It means that I'm going to war." Jack and Mickey both nodded, like they had enough information and they were coming along with him even if he hadn't had the chance to ask them. He turned and faced Sarah. "I can't ask you to come. You've got Luke and Emma would never ever forgive me."

"No better reason to go to war," Sarah said with an understanding nod, and the Doctor nodded as he wondered when she had gotten so wise and how she always managed to be able to read his different faces. He turned to face Martha.

"I want you to come in case Emma's hurt. I won't make you though." He looked towards Jack and Mickey. "Any of you."

"Good luck trying to talk me out of it, boss," Mickey said with a little salute which Jack copied. The Doctor raised an eyebrow up at both of them before looking back at Martha who was studying him carefully. He'd seen her look at him like this after she'd come back from stitching Emma up after the 'Mr. Fear Bubbles' incident, like she was seeing him for the first time all over again. Suddenly he realized that Martha is still comparing how he'd been after Rose and how he is with Emma.

"Of course, I'm coming," Martha said like she hadn't spent several moments studying him closely. The Doctor nodded.

"TARDIS then." Everyone filed in without a word and they left him to fly the TARDIS in silence as they all bent their heads together to discuss what their plan was, as if the Doctor wouldn't agree with their non-pacifist ways this time. The flight was going perfectly well until about mid way through when the TARDIS suddenly shifted direction and the Doctor growled under his breath and lunged for the controls.

"What's happening?" Jack asked and the Doctor growled louder.

"I don't know. It feels like the TARDIS is being summoned." He landed harsher than he probably should have before he stormed to the door and threw it open to the sight of five Ood standing in front of him. "Whatever it is Ood Sigma it is going to have to wait."

"You are going to war for The Girl Touched by Time and we will accompany you," Ood Sigma said and the Ood all took a step forward like there wasn't anything to discuss. The anger that had been flaring up in him at the delay fizzled out as shock overwhelmed him.