Dr. Whooves- Parallel Complications

The Doctor's universe
51st century
Somewhere distant from Earth

Two months. Two months had passed since Samantha had lost the Doctor in the temporal storm. She searched across space and time, checking major historical events on Earth and other planets she knew. The Doctor had given clues to her on how to find him, places to go, old friends of his to talk to, and she had finally found the gem of all clues. That clue led her here, and today she was going to talk to the Doctor.

The city she was in did not have a friendly feeling. The city was black in every form; the buildings were old and rusted, a mild haze filled the streets, and Samantha found herself surrounded by black market dealers and other aliens that looked even more suspicious. Despite this being the exact opposite kind of place the Doctor would want to visit, this was a perfect place to hide.

Samantha continued to wind her way through the streets, avoiding any crowds and heading straight for where she needed to go. She approached a small building, guarded by a gate and a rather large, muscular man with red skin. She had no idea what kind of alien it was, but right now she didn't care.

The man held out a hand, stopping Samantha's movement. "What do you want?" he asked, his voice deep and menacing.

"I need to speak to the Doctor."

***

The Doctor's Universe
2013
Earth
UNIT Headquarters

"Nnngh..."

The Doctor slowly awoke, his entire body aching. He tried to stretch, and discovered that something was latched on to his hooves. He could move, but not much. He was chained down.

"Wha..."

Still groggy, the Doctor opened his eyes, seeing the specially adapted restraints that were holding him in a metal chair. He was in a small room, well lit, one door, no windows. There was someone in front of him, a woman, but his eyes were still hazy. He shook his head a bit, clearing himself up, then looked up and gasped at the woman in front of him.

"Don't worry, we have no intention of hurting you unless you give us reason," Martha said. "I'm Doctor Martha Jones. I work for an organization called UNIT, and our job is to protect this planet. You came to this planet unannounced, and when you did we detected a massive energy reading. We just want to ask you a few questions, then you're free to go."

"Good old Martha Jones, keeping things peaceful around here still," the Doctor replied, smiling.

Martha leaned back, confused by the seemingly personal response. "I'm sorry, I don't think we've met."

"Well, you haven't met me like this yet. The last time I saw you I was saying goodbye, really. I was dying, it was time to start over again, and I wanted to do a farewell tour. You were running about with Mickey Smith, fighting a Sontaran. It's a good thing I always carry a hammer with me."

Martha's eyes slowly widened as she listened to the story she was being told by the alien in front of her. She slowly leaned in, looking into this talking pony's eyes, now seeing how old the eyes looked. "...Doctor?"

"Martha Jones, great to see you again."

Martha gasped, reeling back in her chair and clasping her hands to her mouth for a moment. "Oh my god, Doctor! I can't believe it's you!" Martha jumped out of her chair, more excited than she had been in a long time. "I haven't seen you in... hold on..." Martha's smiling face turned in to a serious one again, and she crossed her arms as she leaned against one of the room's walls. "You turned into a talking pony."

The Doctor blushed, and shrugged slightly. "Yeah..."

"You're joking."

"No..."

"Do you ever stop getting more ridiculous?"

"Oh, if you think this is ridiculous, you should hear about how I saved a griffon kingdom from a plague of beetles using a banana."

Martha dropped her fake serious attitude, chuckling as she grinned at the Doctor once more. "Well, I don't think these restraints are necessary anymore." Martha walked to the Doctor's chair and released all of the restraints on the Doctor's hooves.

"Ah, that's much better," the Doctor said, stretching out and getting in to a more comfortable position on the chair. "So Martha, what have you been up to since we last met?"

"Oh, I left UNIT for a while, I actually married Mickey Smith, then decided to come back to UNIT and make sure they were still running things properly."

"Really, married to Mickey?" the Doctor replied, surprised. "And yet you're still Jones?"

"Well, I kept my last name," Martha explained. "In case..."

"In case I ever popped in, looking for you?"

"Yeah, shut up," Martha said, giggling. "I understand why you don't visit, but there's still always that hope. So what have you been up to?"

"Oh, I stopped the Time Lords from returning and ending time, rebooted the entire universe, married my best friend's daughter, then got shot by the same woman, met an impossible girl, the usual," the Doctor said. "I had some more of the usual stuff after meeting the impossible girl that I won't get into, and the next thing I know, here I am as a talking pony."

Martha nodded. "Sounds about right. So what are you doing here?"

The Doctor's happy demeanor slowly went away as he let out a sigh. "Unfortunately I'm here against my own free will, I'm not where I need to be," the Doctor explained. "I was thrown into a parallel universe, that's when I got turned into a pony, and I need to get back there. What year is it?"

"2013."

"Now Rose's universe is very similar, only slightly ahead in technology. Which means by now UNIT is likely working on a dimension cannon?"

Martha blinked. "Well, that's supposed to be top secret, but you're still in the files as clear to see and know of anything we have."

"The problem with your dimension cannon technology is that it only works when there are tears in the fabric of the universes that shouldn't be there. It's not powerful enough to allow travel between universes seamlessly, there has to be damage. And I guarantee you, there is damage right now. You're going to start getting results, and I need you to use it to send me back to where I got here from."

***

The man grunted at Samantha. "Well you're in the wrong place then," he said, glaring down at her.

Samantha sighed. "Look, just tell her my exact words. Tell her I need to speak to the Doctor, and I guarantee you she'll let me in."

The man rolled his eyes, and motioned for another alien to block Samantha's path. He walked inside the building, and in less than a minute, returned with a change of heart.

"It seems you know the magic words," the man said, grunting once more. "Get out of my sight, you're welcome inside."

Samantha nodded, and hastily entered the building, leaving the sense of fear and anxiety she had in the street behind. After a walk through a hallway, she entered a room that was ten times cleaner than the rest of the town. Maps and charts covered the walls, and the woman Samantha was looking for was right there, across the room, sitting with her back turned.

"Doctor, my name is Samantha," Samantha began, slowly approaching her. "I've come to speak to you about an urgent matter."

"Actually, it's professor now, sweetie. But if you're looking for the Doctor, you absolutely have my help."

***

Martha escorted the Doctor through UNIT Headquarters, using her clearance to end up in a large, warehouse style room. Dozens of scientists in white lab coats moved about, working on different pieces of technology, ranging from hand held weaponry to devices that stood as high as the ceiling.

"What's that over there?" the Doctor asked, noticing a light green, half dome shaped object that was at least 150 feet in diameter, with countless lights and computers around the bottom.

"Oh, that's project Emerald," Martha replied. "No idea if we'll even get it to work yet, but don't worry about it, it's not some big space gun."

Colonel Hutchinson came in to view, and he was rapidly approaching Martha and the Doctor. "Dr. Jones, I'd love to hear what this alien told you so that you'd grant him access to a top secret area."

"Colonel, this alien has proven to me that he's the Doctor. He just sort of... became a pony before he got here."

"The Doctor?" Hutchinson was dumbfounded.

"Yes, hello Colonel," the Doctor said with a smile, holding out a hoof. The colonel hesitantly squatted down, taking the hoof into his hand and shaking it gently. "Seriously long story to explain this, but you know Martha's history I assume. If anyone can give you assurance that I am the Doctor, it's her."

"Well then... if you're the Doctor, I guess that's alright. Welcome back, sir." The colonel stood up again, and gave a salute to the Doctor. "I just saluted a pony..." he said under his breath.

"Anyways sir, the Doctor wanted to have a look at our dimension cannon," Martha explained.

"Certainly Doctor, but may I ask why?" the Colonel moved next to Martha, beginning to walk with her and the Doctor while leading the way.

"This universe is in danger, along with every other parallel universe out there," the Doctor began. "The universes have begun to tear, leaving openings that can never exist. I was pulled into an alternate universe where I was turned into a pony, and that's where the TARDIS is. I need to get back."

"We are glad to help, Doctor," Hutchinson replied. "However, we are only barely beginning to understand the science behind parallel worlds."

"Some worlds are... closer than others, is the only way I can think to describe it, the scientists working on it could explain it better than me," Martha said. "We've been able to actually take some readings from the universe Rose Tyler is in, and minimal readings on some universes farther away, but only with more power put in to the system. Do you have any idea how far away your universe is? Or even a way for us to pinpoint it?"

"I can tell you this universe is farther than I've ever imagined," the Doctor said. "But don't worry, I have a plan."

"You do?"

"Well, I don't know the end bit, but I know the first few steps, and that'll have to be enough. Ah, here it is!"

The Doctor looked up at was simply an undecorated white cube, not nearly as large as the project Emerald that Martha had pointed out, but still large. All the intricate mechanics were inside, and several scientists were making scans and running tests.

"Alright, time to start fiddling. Oh, Martha, you confiscated the device on my hoof, that's my new sonic screwdriver. Can I have it back?"

"Of course, Doctor, I'll run and get it for you."

***

"Professor Song then, sorry. The Doctor told me a lot about you, so I know that things end up in the wrong order. He told me you'd be a good one to come to if I needed help, and I finally found you. The Doctor's gone missing," Samantha explained.

River turned around, smiling at Samantha. "Well neither of us have met, so apparently we meet each other in the proper order," she replied. "Actually, the reason I came to this place is for the same reason you did. A couple months ago, I was going on an archaeology expedition, I wanted to call the Doctor. I didn't get an answer, and that never happens. I came here to hide away and dedicate all my time to searching. All my archaeology team has is my phone number, and every now and then I meet them for missions."

Samantha paused for a moment before responding. "Well, if you meet in the wrong order, couldn't you just find him in a different time?"

"I never know when my message will reach him. And true, I could have just called him again, but that wouldn't help me find him, the Doctor couldn't cross his own time stream without extreme risk. I apparently contacted your Doctor specifically, and now it's my goal to find him too."

Samantha walked about the room, taking a closer look at all the galaxy maps River had on the walls. "You're certainly thorough," she commented.

"I'm always thorough when it comes to dealings with the Doctor," River replied. "And you can take that sentence any way you like, they'd all be equally true," she added with a sly grin. "Now, when did you last see the Doctor? Maybe there's some clue that can help us."

"We were on Benzo, hiking the ruby mountains," Samantha began.

"Ooh, he hasn't taken me there yet, I'll have to make him sometime."

"We ran in to trouble, which is what happens half the time we do anything of course, and the TARDIS took damage before we could jump through time."

"Go on."

"We tried to flee, but the Doctor knew he couldn't break away. There was a temporal storm nearby, and the Doctor decided to fly straight in. I used my vortex manipulator to leave the TARDIS, but-"

"Hold on, did you say temporal storm?"

"Yes."

River leaned back in her chair, remembering the events from a couple months ago when she didn't hear from the Doctor. "Well then, I almost know where he is."

"Where?"

"Wherever he is, Jack Harkness is in the same place."

***

The team of scientists that had been working on the dimension cannon were now standing off to the side, watching a talking pony get more done in ten minutes than they could do in months.

Martha approached the Doctor, who was using his sonic screwdriver to make more adjustments on the control computer. "Doctor, the scientists tell me that the scanners are working a lot better, and they'd be confident in testing a jump. Should they?"

"No no, no one is risking their life for me, I'll be the one to make the jump," the Doctor replied.

"But even with these adjustments, we still can't pinpoint the universe you're from, it's too far. Do you have a plan?"

"I do, but not one I understand," the Doctor replied. "I only just found out about this... universe... energy... stuff," he explained. "I still have no idea how it works, but Chaos said he couldn't kill me directly because I had too much universe energy going through my body. If I'm still a pony then I must have some of the alternate universe's energy field affecting me, and if this machine is smart enough to detect the difference between whatever frequency I'm at and this universe, than it should exponentially reduce the power needed to find and pinpoint the pony universe, then all it takes is a jump."

Martha shook her head slightly. "Ok, a lot of stuff there that I didn't get, but I think I got most of it."

"You asked a complicated question, so you got a complicated answer."

"Alright, how about a different one that I've been meaning to ask, what is that hourglass on your hind leg?"

The Doctor blushed. "Oh, that? That's my, uh..." the Doctor said the name, but not nearly loud enough for Martha to hear.

"Your what? Did you get a tattoo in the other universe? Hour glass, time lord, matching up?"

"No, it's not a tattoo, it's my... cutie mark..."

Martha burst out laughing. "Your what? This is too rich!" she said.

"Oi, I didn't come up with the name, it just showed up there!” the Doctor replied.

"It sounds like something from a little girl's cartoon."

"Well I'm not a little girl, so you can forget that theory."

The Doctor returned to fiddling with the dimension cannon, and after a few more minutes, took a deep breath. "Alright, I have no idea what the physics behind this universe energy thing is, so hopefully a wild guess will be enough for this machine." The Doctor raised a hoof, and gently placed it on a touch sensor.

The machine began to hum loudly, and the Doctor took a step back. An error message came on the screen, and the Doctor stepped forward again, groaning.

"Do you need more time?" Martha asked.

"Actually, the machine managed to detect the underlying universal energy field from this universe after it scanned me, so you can now say that UNIT were the first people to discover this energy field thingy, not even the time lords knew of this," the doctor said. "And it looks like it can set up a lock with this universe and mine, so that travel can be made back and forth. Once the lock is in place jumping will be easy, but I'll need a lot more power to activate the lock."

"How much more?"

"Um... about a fifty mile radius around this building. That much."

Martha blinked, nervously nodding. "Well, when the entire universe is in danger, I can get some people to formulate a cover up for why there's a power outage of such a large area,"

"Brilliant, let's get ready then."

***

The pony universe
Earth
Canterlot castle
30 seconds after the Doctor's disappearance

Paige sat in stunned silence, and Jack paced back and forth, neither with any clue of what happened to the Doctor or how to get him back.

"Is there anything you can do, princesses?" Jack asked. "If we don't have the Doctor, there's no way we can fight whatever this thing is."

Celestia's look of sadness changed into a smile. "Oh, just wait a few more seconds," she replied.

"Wait, what?"

"Doctor, you can come out now."

***

The Doctor's universe

A scientist placed a necklace with a large, yellow button attached around the Doctor's neck, the dimension cannon now ready and fully functional.

"Well Martha, it was a pleasure seeing you again," the Doctor said, smiling up at Martha.

"I know that I'm the one who left, but it was great seeing you too," Martha replied. "Oh, come here, you talking pony time lord."

Martha knelt down and pulled the Doctor in for a hug, which the Doctor returned with the one front hoof he could manage to get around to Martha's back. "As long as I can prevent an extremely powerful creature from destroying every parallel universe in existence, I'll start popping in from time to time."

"Sounds like a plan," Martha said, chuckling as she broke from the hug.

Colonel Hutchinson stood nearby, and gave the Doctor a salute. "Always a pleasure for UNIT to help the Doctor, sir," he said.

The Doctor returned the salute. "Thanks for not assuming I was hostile. Otherwise I might be dead by now."

"Don't worry Doctor, I'll keep these guys in check," Martha said.

"Alright, well, here goes nothing. See you around, Dr. Jones. Say hi to Mickey for me." With a press of the button around his neck, the Doctor was gone.

***

The pony universe
Earth
Canterlot Castle
4 hours before the Doctor was teleported

Celestia sat on her throne, reading a scroll and enjoying the quiet day. She looked up when a guard entered through the large double doors at the end of the room.

"Princess, there is a pony outside who says he should be let in. He didn't give a name, he just says he's a doctor."

Celestia lit up, and set down her scroll. "Let him in at once. He can be trusted."

When the guard returned, the Doctor was with him, smiling widely. "Hello, princess! I'm back!" he shouted.

"Yes, it's wonderful to see you after 300 years," she said.

"Oh, right, I'm back, but I'm also not back, I will be back, it's complicated," the Doctor said. "I was teleported all the way to my own universe, and I was still a pony! I got back, but the time wasn't quite synced when the lock was set, now this blasted thing is broken. No matter, I've got readings from my universe stored in here so the TARDIS can work out the kinks and travel back."

"You don't have the TARDIS? How did you get here then? And you were teleported back to your universe?" Celestia replied.

"I teleported to where UNIT headquarters would be if it was here," the Doctor said. "But I found a man with a rigged gambling game, reversed the rig on him to get enough money for a train ride, and here I am. Ta da!" The Doctor stood up on his hind hooves for a moment, smiling widely. "Anyways, you have a lot of questions for me princess, and unfortunately I can't answer them right now. But don't worry, you only have a few hours to wait. Some sad things are going to happen I'm afraid, I can't mess with my own timeline. Is it alright if I hide for a few hours until I show up again?"

Celestia was thoroughly confused, but trusted the Doctor when he said she would understand soon. "Alright Doctor, we can chat for a while, then you can hide just behind the door over there when the necessary time comes."

***

4 hours and 30 seconds later

"Doctor, you can come out now."

The Doctor emerged from a door behind Celestia's throne, grinning widely. "Ta da! I like ta da, it's invigorating, I think I'll say ta da more."

"Doctor!" Paige shouted, rushing up to him and beaming. "But, how did you get back?"

"I was teleported to my own universe, but I found a way back. I got here early, so I had to wait around. Time travel, things can get tricky," he said.

"Well you were right, Doctor, I understand now," Celestia said with a chuckle. "Although I wish I could have helped."

Don't worry Celestia, when I got here things had already happened in my time stream," the Doctor said.

"So what do we do now?" Jack asked.

"There's some searching I need to do. I need more answers before I can go after Chaos, and I came up with a thought on where to go while I waited," the Doctor said. He turned back to princess Celestia. "But don't worry princess, I promise you that I will find Chaos, and stop him, no matter what it takes."

"I have faith in you Doctor, and I am eternally grateful," Celestia replied.

"Alright then, Jack, Paige, onwards. We need to go back in time," the Doctor said. "Until next time, princesses."

Both Celestia and Luna gave a nod, and the Doctor entered the TARDIS with his companions, ready for another trip.

***

The Doctor's Universe

"Wait, you know Jack Harkness?" Samantha asked.

"Not until recently, do you know him?" River replied.

"I've never met him in person, but I'm surprised you know him," Samantha said. "The Doctor always told me that his two favorite people in the universe were the same two people that could never be in the same room."

"Indeed, I see now why the Doctor has kept that man from me for so long, I think he's worried about Jack being competition for him. I’d never leave the Doctor, but Jack is certainly the most tempting man I’ve ever met," River joked. "I knew of Jack Harkness, but he didn't know of me. So I kept quiet about my knowledge of the Doctor, and got him tagging along on archaeology expeditions with me. Eventually the Doctor came up on accident, he already knew that the Doctor was married but didn’t know to who, and we exchanged stories. He ended up in a temporal storm a little while ago, just like how you said the Doctor disappeared. What does your Doctor look like, by the way?"

"Tall, blonde, grey suit."

"Ah, I haven’t met that one but I’ve seen pictures," River explained. "A while ago a version of the Doctor I’d rarely seen, one from farther in his timestream, taught me how to detect and identify temporal storms, but I never knew why until now. The temporal storm that hit Jack was by chance, but we could find one with what he taught me."

"And if we find a storm, we might be able to find the Doctor?"

"Yes."

"Let's do it then."