So, my very first, multichapter, 11th Doctor story. It took me a full 2 seasons to try my hand at this. Here's hoping I've gotten the hang of this Doctor's personality. If not, I'm sure I'll be chastised in the reviews.

I'm aiming for a chapter a day until the end of the year, 11 chapters total, with a bonus section to be posted on New Year's Day. Please enjoy and leave reviews to let me know this didn't go to waste. I spent something like 6 months pulling it together so that I could post a completed story.

Edit: 1-5-12. Added disclaimer, which I can't believe I forgot in the first place. Minor punctuation changes.

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Plot Summary: On Matrix Prime, people can hook themselves up to machines and live out their fantasies. But it comes with a cost: the life energy of the people. They live out their fantasies, which may take place over years, but in reality, their bodies wither away quickly.

When Amy, Rory, and the Doctor visit, they are tricked into hooking into the Matrix. Now it is a race to separate fantasy from reality and a fight to free the Doctor, if Amy and Rory can free themselves first.

Takes place after "Let's Kill Hitler" but anytime before "The Girl Who Waited."

References: The Matrix, Surrogates, Repo Men, Batman Forever, Star Trek: Generations

Doctor Who: Amy's Choice, the Rebel Flesh/Gangers

DISCLAIMER: I do not own Doctor Who, which includes any and all references made to people/places/items owned by the BBC. I own all OC chars and species presented for this story.

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Preface

Three figures were walking on a ramp, one at a brisk pace, the other two a little slower as they gazed around in wonderment. Rows upon rows, stacks upon stacks of people lying in tilted tubes, sleeping. Monitors beside each tube showed their vital signs and how long they had been there.

"Won't this be wonderful?" said one, a woman, gushing. "It's been twenty-five years since our honeymoon and we'll be back on that lost planet, literally like it was yesterday."

"That's nice, honey," said the other, a man, her husband apparently. He was a little disconcerted at the sleeping people, clad only in a simple white gown.

"Oh, for heaven's sake, Harvey, you could be a little happier!" she snipped. "This is a once in a lifetime opportunity! It was lucky I found this place!"

He shrank back a little. "Sorry, Flo. I just don't have a very good feeling is all."

They arrived at two empty tubes. The figure that had led them there, a small humanoid creature about three feet tall and a sort of orangey color, held out a webbed hand for Flo to grasp as she climbed in, her dark hair carefully tucked behind her head. Beside her, Harvey clambered in without assistance, shaking his head. To their temples, the creature stuck disks with wires trailing from it.

"Not a good feeling at all."

With a hiss, the tubes slid shut. A gas began to fill the tubes as the couple relaxed. Within seconds, they were breathing at a slow, even pace.

The creature looked up. Above, hidden in an alcove, a figure nodded. The creature began to turn dials and press buttons.

In the tubes, strands of Flo's hair began to turn white.

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(Amy Pond voiceover)

When I was a little girl, I had an imaginary friend, and when I grew up, he came back.

He's called the Doctor, he comes from somewhere else, he's got a box called the TARDIS that's bigger on the inside and can travel anywhere in time and space.

I ran away with him and we've been running ever since.

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MATT SMITH

KAREN GILLIAN

ARTHUR DARVILL

DOCTOR WHO

MYSTERY OF THE MATRIX

by

Jennifer R. Song

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Chapter 1

THWACK!

DING!

HISS!

"OW!"

It was to a myriad of loud sounds that the Ponds walked into. At the moment, the Doctor was trying to drive the TARDIS with his left hand and was sucking on two fingers on his right. When he noticed Amy and Rory, he swiftly yanked his fingers out and wiped them on his pants.

"Oh, morning!"

"Mornin' Doctor," said Amy. "What did you do the TARDIS to make her burn you?"

"Oh, I thought she needed some recalibrating, she thought she didn't, and let me know so."

Another hiss from the console seemed to be the old ship's way of both confirming and warning him not to do it again. The Doctor tried to glare at the console, but his concentration was broken by the column suddenly stopping.

"We've landed," stated Rory, now used telling the difference between being in flight and being solid.

"Any idea where?" asked Amy.

The Doctor pulled the computer screen around and pressed a button. "Matrix Prime. 32nd century, roughly. This place is known for its in-depth virtual reality. Perfect way to have a holiday without risking your life."

Amy rolled her eyes. "Boring."

"I dunno, what if you wanted to skydive?" asked Rory. "I mean, I wouldn't, you know, in reality. But virtual? You don't get hurt, you can't die, but you get the whole adrenalin thrill."

The Doctor pointed triumphantly at Rory. "See? He's got it. Let's go!"

With a bound, he was out the door.

"I swear, for someone that's hundreds of years older, he's about as eager as a kid in a candy store," muttered Amy.

"Not arguing."

The Doctor stuck his head back in. "Come along, Ponds. We've exploring to do."

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They had parked in a small closet, which, when they emerged, found themselves in a large, completely white waiting room. It was completely silent, except for a single humanoid in the middle of the room. Its orange skin and matching hair stood out from behind the transparent computer screen it was situated behind. Rory's shoes squeaked as they approached…him? Her? It? The creature looked up.

"Name." The voice was, more or less, feminine.

"Oh, hello, I'm the Doctor, this is Amy and Rory–"

"Appointment?"

"Ah, no, we're just dropping by, you know, thought it'd make a nice vacation."

She looked at him through the screen. Blinked. Then pressed a button on the desk. The buzz echoed loudly off the walls.

A door appeared from nowhere on the white wall. Three of the orange creatures came out, dressed in some kind of white uniform.

"You will go with them."

"If this is your idea of security, not much," said Amy as one grabbed her by her right hand and yanked her along.

"Um, Amy, I don't think they're security," said Rory as another grasped his left hand and pulled him after her.

"No, they're not," concurred the Doctor, sidestepping the last one and quickly striding to catch up to his companions.

They were led up a winding path. Sometimes, doors would open from the walls, allowing them to see more of the creatures at work as they came and went. Some were computer rooms, projecting unintelligible data. Others were repair rooms, where they could see long, slender tubes being disassembled or reassembled. A few had experiments going in, if the smoke and bubbling from what looked like Buson burners were any indication.

Finally, they reached a frosted pair of doors, unique in that while the other doors had been invisible until activated, this pair clearly was meant to draw attention.

"Oh, goody, whoever is in charge," said the Doctor, grinning.

The doors slid open.

"Ah, welcome, welcome."

A middle-aged man, slightly balding, came running up to them. He pumped their hands excitedly.

"We were beginning to think you wouldn't show up."

"We're expected?" asked Amy.

"Well, of course," said the man. "Oh, how rude of me, my name is Benedict. Benedict Cummings. And you are?"

"I'm the Doctor, she's Amy, he's Rory." The Doctor spread his hands out. "Here as requested."

Benedict nodded his head, breathless. "Yes, I've requested that they send diagnosticians again and again. But they keep saying they can't spare a soul. Well, looks like they managed three, eh?"

He clapped the Doctor on the back.

"Let's get you three down to the testing room, shall we?"

Amy and Rory had enough time to send each other a look of uncertainty before the little creatures poked them into following Benedict.

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The room was quiet, save for the soft hum of machinery. A dozen mostly gutted tube devices were linked into a wall, computers plugged into them flashing red and green lights. Two of the creatures, wearing lab coats, were studying the results.

"We've been having a bit of an issue with some of the VR-pods. There's some kind of, almost virus, in the system."

"Almost virus?" queried the Doctor.

"Well, most of the time it registers on the system as a valid program, which was actually put in, I checked with the manufacturer. And then sometimes, it pops up as a high-threat virus and demands that some programs be deleted for the safety of the system."

"How are you still running the place, then?" said Amy.

"Oh, it's only a small percentage of VR-pods that are affected, about 5% at the most." He gestured at the row. "This is one set of about, oh, near 50 affected."

The Doctor took out the sonic screwdriver and began scanning the devices. One of the orange humanoids squealed in horror.

"No, no, no, it's ok, see, just scanning."

It relaxed, seeing as the device had not interfered with their work.

Rory spoke up. "Um, Mr. Cummings? What are these guys called?"

"Benedict, please. And they are called Zharytes."

Amy snorted. "Look like Oomaph-loopas to me."

"Amy," said the Doctor warningly.

"Sorry. They just do."

"Unfortunately, their home planet was destroyed in a freak supernova a few centuries ago. The only ones left are here on Matrix Prime."

The Doctor kept silent as he continued to scan. Another race, another world lost because of him and the Time Lords and the Time War.

His contemplation ceased as he realized the only way to actually deal with this problem.

"We're going in."

"Sorry, what, it just sounded like you said we're going in," said Amy. Her time spent in the birthing chamber had caused her to be a bit more claustrophobic than usual. "If there's a computer problem, the last place we wanna be is inside, right?"

"Wrong, 'cause if there's a problem in there, we can find the problem and fix it from the inside." He turned to Benedict.

"Time to plug in."

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"Okay, there will be some slight discomfort as your system adjusts," said Benedict, hooking up Rory to one of half a dozen, definitely put back together, VR-pods. Amy was fidgeting with a temple pad. It itched. And that not-so-nice stomach lurching wasn't helping either. "You'll just need to relax, and let your mind float free. Oh, and you might experience some, ah, other issues we haven't yet been able to sort out."

"Ready, Ponds?"

"Nope."

"Nu-uh"

The Doctor grinned. "Neither am I."

A brilliant light.

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There's the set up. So what do you think their fantasies will be?