To avoid any continuity errors as I wrote this after Time of Angels aired, but before Flesh and Stone, this story is AU from Flesh and Stone. Or something.
"Have you ever learned how to drive a car?" Amy asked as she held on to the rails for her dear life.
"Yes. Why?" the Doctor called from the other side of the TARDIS console. He was busy turning knobs and flipping switches.
"Because you don't use the stabilizers on purpose. It gets a bit bumpy in here."
"It's a mauve alert. Intergalactic equivalent for red alert. That's where you humans get red from. Long long time ago, back when UNIT was formed. Sometimes Earth can be so unoriginal, but camping. You lot are the only ones who do that!"
"Alert? What's wrong?"
"Don't know," the Doctor marveled. "Let's find out shall we?"
"So where are we now?" Amy stepped out and saw nothing but dingy high-rises and muck filled streets with hover cars.
"New Earth," the Time Lord remarked, coming out of the TARDIS. He snapped his fingers and the door closed.
"How do you lock it?" Amy asked.
"Lock what? The TARDIS? She's clever enough to not let her get stolen. She's alive you know."
"She's a she?"
"Well humans called their ships 'shes' don't they?"
"But you had a key before."
"Way back when. Don't need it anymore. Here ya go." The eleventh Doctor tossed the golden key to Amy. "More use of it for you now. Don't lose it."
"Why me?"
"Why not you Amy Pond? Amelia, Amelia, Amy Pond."
"Alright, stop that. It's getting a bit irritating."
"Am I irritating?"
"Sometimes, maybe."
"Not rude though?"
Amy shrugged. "We're in the future? Looks like Starship UK."
"It's way earlier than that. I'd say only one thousand years from 2010, but based on the smell of the air… we're on the other side of the galaxy from where Starship UK stood."
"You can tell that from the smell of the air?"
"Pollution levels. Not hard. Oi wait. What's that?" The Doctor pointed off into the distance.
"Looks like a fight."
"Well then. Come on!"
"Wait!" Amy shouted after him as they ran towards the scene. She stopped against the Time Lord's outstretched hand. She followed his gaze to the scene. There were at least five bandits, undoubtedly human besides the fact that they were genetically altered to have abnormal body parts. In the center was one man trying to fend them off. Amy watched in horror as the man injured and killed all five.
"He wouldn't do that," the Doctor whispered. He was unaware that Amy heard him. "Let's go. Now." He turned around with the intention of running back to the TARDIS behind the hill but shouted as a self-programmed military weapon flew straight towards him. He ducked along with Amy as the other man shot down the weapon.
"Hey!" the man cried. "What the hell do you think you're doing?"
The Doctor got up and smiled feebly, knowing there was no way out of this situation. "Hello! Sorry for the trouble."
"You don't want to be out here during this time of day when there's war going on." The man approached them and Amy could feel the Doctor stiffen. Was he afraid? Surely the mighty Time Lord couldn't be scared of one man.
"Yeah. Like I said before sorry."
"Who are you? Never seen the two of you around."
"I'm…" the Doctor searched for a suitable name. "William Clark," he finally came up with. "This is Amy Pond. We grew up together."
"Childhood friends?"
"Something of the sort."
"Nice to meet you," the man nodded. "Captain Jack Harkness."
"Captain? Of what?" Amy asked.
"Amy, that's rude to ask. He probably doesn't want to tell you," the Doctor whispered.
"The title used to mean something. Now it doesn't. Come on. Let me get you to the Silo."
"Silo?" the Doctor remarked at the familiarity of the name.
Amy marveled at the complexity of the underground haven. There was still electricity and running water, as well as food and other scavenged necessities. She didn't understand why the Doctor was afraid of this man. He was nice enough to them, even giving them a bedroom. The Doctor had to ruin the moment by pulling out his knowledge.
"What's that?" the Time Lord asked, nodding to the box on the wall.
"Transducer," Harkness replied. "Sometimes the Silo doesn't get enough electricity. We have to fine our own ways to power up this place up."
The Doctor peered at it closely. The covering was transparent, revealing circuit boards and wires beneath the control buttons. "Looks wired enough to set up an explosion. Look at that, parallel circuits wherever you can fit them. Guaranteed energy. And Silo? Where did you come up with that name? Wasn't that something used for storing grain in the ancient times?" Harkness raised his eyebrows while Amy visibly rolled her eyes. "I'm a scholar," the Doctor supplied.
The captain nodded in understanding. "Then you wouldn't mind helping my team?"
"You've got a team?"
The man led them up to the end of a hallway. There was nothing but a big brick wall. "There's nothing there," Amy pointed out.
The corner of your eye, the Doctor thought.
Harkness laughed. "That's where you're wrong." He pushed up his sleeve and pressed a few buttons on his wrist strap. "Welcome to 31st Century Torchwood."
The brick had rippled away to reveal the most amazing secret headquarters Amy Pond had ever seen in her life. It was just like the films. All polished silvery and glittering. "The stars are like diamonds," the Doctor muttered.
"What was that?" Amy asked.
"Nothing," the Time Lord dismissed quickly. "So Torchwood," the Doctor exclaimed loudly. "What's that?" While he was speaking, three people –one man and two women- came out. All were very young.
"William Clark and Amy Pond, meet Rhea, Miriam and David. Torchwood. We fight aliens."
"That's interesting. You a secret to the world? Never heard of you."
"We try to be undercover," Harkness replied.
"Worked for me." The Doctor flashed a smile.
"What's he doing here?" the man named David asked.
"More importantly who is he?" Rhea put in.
"Everyone, meet William Clark and Amy Pond," the captain introduced. "Apparently William here's a bit of a genius."
"He's just exaggerating," interrupted the Time Lord.
"He's here to help."
"With what?" Rhea inquired.
"Yeah Captain," the Doctor agreed. "Still don't know what I'm signing up for."
"And why are their clothes clean?" Miriam finally asked.
Everyone turned to stare at them, noticing the obvious for the first time. Usually the survivors that were found had shabby clothes. A rip in the pants here, a scorch in a shirt there. And they most definitely did not dress in layers. On top of that, they had bruises, cuts and scrapes all over them. These two, however, did not.
"Uh, well," the Doctor began. "Always quick on our feet. This isn't the first time we've been in a crisis before. You learn to survive after a while don't you?" The Doctor must have given an honest answer because the Torchwood team accepted it easily. Amy cast her Time Lord friend a quizzical glance. The Doctor just looked back and looked away quickly.
"Come on," Harkness said. "I'll show you what you'll be helping us with."