Three weeks off and plenty of time to space, therefore, I have decided to watch all of series 1-10 of new who and have come up with a brilliant idea for a small project. I never wrote the Ninth Doctors series, it never fit with my plot but what if the Stone never became Rita Stone? What if she left with the Doctor during the Time War?

What do you think? It would only be series one of course but an AU where the Stone survives? I think it would be fantastic.

-----

"Works in quadrants. Every movement sensor and trip light we've got." Mack said as the Doctor and the Stone reentered the church after setting the last cameras in place. "If anything moves, we'll know."

"Good lad." The Doctor nodded before heading back out with the Stone to find Ambrose's meals on wheels van.

"Oi! What're you doing?" The woman exclaimed while the Doctor dug into the driver's side of the van.

"Resources." The Stone answered like it was obvious.

"Every little helps. Meals on wheels." The Doctor nodded in hum then opened the back poking his head in with the Time Lady. "What've you got here, then. Warmer in the front, refrigerated in the back."

"Bit chilly for a hideout, mind," Ambrose muttered, the Stone frowned hearing a clatter of items as Ambrose turned to them after looking in the front seat.

"What are those?" She questioned raising a brow while the Doctor looked.

"Like you say, every little helps."

"No, no weapons." The Doctor shook his head. "It's not the way we do things." He pointed at himself and the Stone.

"You said we're supposed to be defending ourselves." She protested.

"Oh, Ambrose." The Stone slowly shook her head.

"You're better than this." The Doctor added a hint of a harsher tone in his voice. "I'm asking nicely. Put them away."

---------------------------------------------------------

"Look at that." The Doctor grinned holding up Elliots map. "Perfect. Dyslexia never stopped Da Vinci or Einstein."

"And it's definitely not stopping you." The Stone smiled patting his head.

"I don't understand what you're going to do." He frowned.

"Two-phase plan." The Doctor went on to explain. "First, the sensors and cameras will tell us when something arrives. Second, if something does arrive, I use this," he held up his sonic. "Send a sonic pulse through that network of devices. A pulse which would temporarily incapacitate most things in the universe."

"Knock 'em out. Cool."

"Lovely place to grow up round here." The Stone hummed the Doctor nodded in agreement.

"Suppose." He shrugged. "I want to live in a city one day. Soon as I'm old enough, I'll be off."

"I was the same where I grew up."

"We both were, sweetheart." The Stone chuckled.

"Did you get away?"

"Yeah." The Doctor nodded taking the Time Lady's hand.

"Do you ever miss it?"

"So much." He squeezed the blonde's hand glancing over at her seeing the small amount of hurt in her eyes, not because of the boy but memories.

"Is it monsters coming?" Elliot asked looking at the screen. "Have you met monsters before?"

"Yeah."

"You scared of them?"

"No, they're scared of my wife." He grinned.

"And you sweetheart." She chuckled. "They get very scared of you."

"You know I don't understand why because I'm a sweetheart according to you." He beamed.

"Ah but you're my sweetheart, not theirs."

"Well, there is that."

"Ah yes." The Time Lady lightly coughed seeing Elliot looking between the two of them.

"Will you really get my dad back?" He asked.

"No question." The Doctor nodded.

"I left my headphones at home." He called running out of the church.

"I'll go with you!" The Stone called over her shoulder. "Can't let him go alone." She kissed the Doctors cheek. See you later sweetheart."

"Be careful dear." He whispered to her.

"Oh, I'll always be careful." She winked then headed off.

---------------------------------------------------------

"How're you doing?" The Doctor asked Rory who was looking at a sensor array.

"It's getting darker." He frowned How can it be getting dark so quickly?"

"Shutting out light from within the barricade." The Doctor answered. "Trying to isolate us in the dark. Which means..." there then was a loud rumble. "It's here."

---------------------------------------------------------

"Oh, that can't be good." The Stone murmured exiting the house with Elliot."

"Why is it night?" He questioned.

"It's not." The Stone said licking her finger then raising it in the air before flashing her sonic in the air. "They're trying to keep us in the dark, I presume to make us scared, something like that."

"I'm not that scared." Elliot frowned.

"No your right, perhaps they're trying to scare adults... possibly."

"But your an adult."

"I'm older than you would possibly imagine or believe." She smiled. "But no I'm not that scared, not really because I'm not afraid of the dark... well the Vashta Narada I am but the harmless dark, nope."

"Vashta what...?"

"Narada."

"Vashta Narada?"

"Savages of the dark." She shrugged.

"Oh." He blinked stepping a little closer.

"Yeah..." she slowly nodded making a mental note to rethink her words a little more. "Let's get you back I'm sure your mother is worried about you."

---------------------------------------------------------

"I can't open it," Ambrose said trying to pull open the church door. "It keeps sticking. The wood's warped."

"Any time you want to help." The Doctor called over his shoulder to Rory.

"Can't you sonic it?"

"It doesn't do wood." He protested.

"That is rubbish."

"Oi, don't diss the sonics." The Doctor narrowed his eyes at Rory.

"I'm working on it. Now please help us." The four forced the door open using their shoulders to push on the door.

The ground then started to shake even more than before and objects began to fall. "See if we can get a fix." The Doctor started to type on the computer. The lights the exploded while the computer sparked making the Doctor jump back.

"No power," Mack muttered.

"It's deliberate." The Doctor informed.

"What do we do now?" Rory asked.

"Nothing." The Doctor sighed. "We've got nothing. They sent an energy surge to wreck our systems."

"Is everyone okay?" Rory questioned. "Is anyone hurt?"

"I'm fine." Nasreen nodded.

"Me too." Ambrose informed. There was then a larger rumble.

"Doctor... what was that?" Rory questioned

"It's like the holes at the drill station."

"Is this how they happened?" Nasreen asked.

"It's coming through the final layer of Earth." The Doctor muttered pressing his ear against the floor.

"What is?" Nasreen asked jump before the room fell silent with no rumbling or items falling.

"The banging's stopped." Mack frowned.

"Where's Elliot?" Ambrose worryingly asked looking around. "Has anyone seen Elliot? Did he come in? Was he in when the door was shut?" The Doctors eyes widened realising who else wasn't here. "Who counted him back in? Who saw him last?"

"I did." The Doctor swallowed.

"Where is he?"

"He said he was going to get headphones."

"And you let him go?" Her eyes widened in even more horror. "He was out there on his own?"

"No." The Doctor shook his head his eyes snapping to hers. "He's with the safest person I know, she won't let anything hurt him trust me."

"Who's he with?" She frowned.

"Doctor...?" Rory frowned. "Where's the Stone?"

---------------------------------------------------------

"Mum!" They heard Elliot shout from outside the door. "Grandpa Tony! Let me in!"

"Elliot!"

"Let me in."

"He's out there." The woman cried running to the door trying to open it. "Help me!"

"Open the door." He screamed banging on it. "Mum! There's something out here."

"Where's the Stone!" The Doctor worryingly shouted not hearing her at all or feeling the Time Lady in the back of his mind.

"Push, Elliot!" Ambrose cried out. "Push, Elliot. Give it a shove."

"Something took her!" He shouted. "Mum. Hurry up!" The banging then stopped. "Mum." He murmured.

---------------------------------------------------------

"Come on." Mack groaned pulling just before the door swung open.

"Elliot!" Ambrose shouted running out. "Where is he? He was here. He was here. Elliot!"

"Ambrose, don't go running off!" The Doctor shouted his eyes looking around trying to find the Time Lady.

"Ambrose!" Mack shouted running after her.

---------------------------------------------------------

"Dear Rassilon." The Stone groaned rubbing her head. "I only hope my mental shields went up before the Doctor could feel this pain..." She then frowned seeing a glass-like cover. "Oh, this is like a coffin." She muttered raising a brow.

---------------------------------------------------------

"Elliot, it's Mum," Ambrose called before gasping and finding his headphones on the ground.

"No!" She cried out before being knocked over by something. "Get off me!" She cried out. Mack then grabbed it from behind only for the creature to wriggle free and be attacked by its extendable tongue before running away. Dad!"

"What happened?" The Doctor questioned running up.

"My dad's hurt."

"Get him into the church now." He ordered.

"Elliot's gone." She sobbed. "They've killed him, haven't they?"

"I don't think so." The Doctor shook his head feeling the Stone was definitely here and alive. "They've taken four people when they could've just killed them up here. There's still hope, Ambrose. There is always hope."

"Then why have they taken him?"

"I don't know. I'll find Elliot, I promise. He was with my wife the smartest woman I know, she's alive I can feel it I will get them back. But first I've got to stop this attack. Please, get inside the church."

Ambrose swallowed nodding. "Come on, Dad."

Rory frowned. "So what now?"

---------------------------------------------------------

The Stone frowned hearing a faint knocking nearby accompanied by a Scottish woman shouting. 'Amy!' Her eyes lit up knowing the woman was alive and that the Doctor wasn't getting killed by Rory today. "Let me out. Can anybody hear me? I'm alive in here!" She heard the redhead shout. "Let me out! I know you're out there. My name is Amy Pond and you'd better get me the hell out of here or so help me I am going to kick your backside." Her eyes widened seeing a green figure over her. "Please?"

"Doctor?" The Stone attempted to telepathically call to him. "Theta...?"

"Stone?" He replied fear seeping into his voice. "Are you okay? Where are you?"

"Sweetheart I'm fine." She quickly reassured. "I'm somewhere in the ground, is Elliot okay? I diverted it away before it could get him, but I didn't see what it was."

"He was taken. I'm sorry."

"But he must be alive." She muttered. "Amy's here as well, alive."

"Oh good." He sighed out a breath of relief.

"I'll see you soon sweetheart."

"Stay safe, dear."

"I'll try, but you know me, Doctor." She grinned knowing that he felt better now. She could tell he blamed himself for what happened to Amy but now he knew she was alive.

"She's alive." The Doctor broke out into a broad smile.

"Who?!" Rory asked his eyes brightening.

"The Stone!" He beamed.

"What about Amy?" Rory whispered his eyes drifting down to the ground.

"So's she." He grinned.

"But how do you know?"

"Telepathic link with the Stone, all Time Lords have it. Ours is only stronger because we're united." He grinned. "So, I think I've met these creatures before. Different branch of the species, mind, but all the same." He clapped his hands together. "Let's see if our friend's thawed out."

"Are you sure?" Rory questioned. "By yourself?"

"Very sure." He nodded.

"But the sting?"

"Venom gland takes at least twenty-four hours to recharge. Am I right?" He called to the creature chained up. "I know what I'm doing. I'll be fine."

Rory slowly nodded and left the Doctor who slowly walked towards the creature with green scales and a grey mask on the floor. "I'm the Doctor. I've come to talk." He slowly knelt down raising his hands to the creatures face. "I'm going to remove your mask." He then slowly took it off showing a reptile like scaly face. "You are beautiful." He whispered. "Remnant of a bygone age on planet Earth. And by the way, lovely mode of travel I bet my wife would love it even more if she was here. Geothermal currents projecting you up through a network of tunnels. Gorgeous." He grinned then grabbed the folding chair on the side. "Mind if I sit? Now. Your people have my wife and a friend of ours. I want them back." He ordered sitting down on the chair. "Why did you come to the surface? What do you want? Oh, I do hate a monologue." He groaned. "Give us a bit back. How many are you?"

"I'm the last of my species."

"Really. No." His eyes darkened. "Last of the species. The Klempari Defence. As an interrogation defence, it's a bit old hat, I'm afraid."

"I'm the last of my species."

"No." He firmly replied leaning forward a little his eyes narrowing. "You're really not. Because my wife and I are the last of our species and I know how it sits in a heart. So don't insult my wife because it won't end well, I don't appreciate my wife being insulted, your also glad she isn't here because otherwise, it wouldn't have been pretty." He then broke into a smile leaning back. "Let's start again. Tell me your name."

"Alaya."

"How long has your tribe been sleeping under the Earth, Alaya?" He asked waiting for an answer before rolling his eyes. "It's not difficult to work out. You're three hundred million years out of your comfort zone. Question is, what woke you now?"

"We were attacked."

"The drill." He murmured.

"Our sensors detected a threat to our life support systems. The warrior class was activated to prevent the assault. We will wipe the vermin from the surface and reclaim our planet."

"Do we have to say vermin?" He frowned. "They're really very nice, plus my wife was stuck as one of them for a while."

"Primitive apes." She sneered.

"Extraordinary species." He corrected. "You attack them, they'll fight back. But, there's a peace to be brokered here. I can help you with that."

"This land is ours. We lived here long before the apes."

"Doesn't give you automatic rights to it now, I'm afraid. Humans won't give up the planet."

"So we destroy them." She hissed.

"You underestimate them."

"You underestimate us."

"One tribe of homo reptilia against six billion humans?" He scoffed. "You've got your work cut out."

"We did not initiate combat, but we can still win."

"Tell me where my wife and our friend are give us back the people who were taken."

"No."

"I'm not going let you provoke a war, Alaya. There'll be no battle here today."

"The fire of war is already lit. A massacre is due."

"Not while I'm here." He darkly warned.

"I'll gladly die for my cause. What will you sacrifice for yours?"

---------------------------------------------------------

"You're going to what?" Rory gaped at him.

"I'm going to go down below the surface, to find the rest of the tribe, to talk to them and to get my wife back."

"You're going to negotiate with these aliens?" Ambrose gawked at him.

"They're not aliens. They're Earth-liens." He corrected. "Once known as the Silurian race, or, some would argue, Eocenes, or Homo Reptilia. Not monsters, not evil. Well, only as evil as you are. The previous owners of the planet, that's all." He explained seeing the woman not convinced he sighed. "Look, from their point of view, you're the invaders. Your drill was threatening their settlement. Now, the creature in the crypt. Her name's Alaya. She's one of their warriors, and she's my best bargaining chip. I need her alive. If she lives, so do Elliot and Mo, Amy and the Stone, because I will find them. While I'm gone, you four people, in this church, in this corner of planet Earth, you have to be the best of humanity."

"And what if they come back?" Mack questioned. "Shouldn't we be examining this creature? Dissecting it, finding its weak points?"

The Doctor instantly shook his head. "No dissecting, no examining. We return their hostage, they return ours, nobody gets harmed. We can land this together if you are the best you can be. You are decent, brilliant people. Nobody dies today. Understand?"

Nasreen started to applause before slowly stopping seeing no one else doing the same.

---------------------------------------------------------

"I'm coming to get you, dear." The Doctor telepathically told the Stone.

"I'll tell Amy to get ready to leave sweetheart, as soon as I'm out of this box..."

"Box?"

"Like a glass case, I don't think they realised that they haven't gassed me yet."

"I'm still gonna get you back and not let you out my sight for a week."

"You're so clingy." She rolled her eyes while he stormed up to the TARDIS not seeing Nasreen following.

"I don't hear you complaining dear." He smirked.

"Oh, shut up."

"No, sorry, no." The Doctor frowned seeing Nasreen. "What are you doing?"

"Coming with you, of course." She grinned. "What is it, some kind of transport pod?"

"Sort of, but you're not coming with me."

"He's right." Mack nodded. "You're not."

"I have spent all my life excavating the layers of this planet, and now you want me to stand back while you head down into it?" She scoffed. "I don't think so."

"I don't have time to argue."

"I thought we were in a rush."

"It'll be dangerous."

"Oh, so's crossing the road." She shrugged.

"Oh, for goodness sake." He grumbled. "All right, then. Come on." He went into the TARDIS sighing and shaking his head.