The Hunt for Doctor Whooves

by Princess Bronicorn

Rating: teen
Tags: Adventure, Derpy Hooves, Princess Celestia, Crossover, Doctor Whooves, Twilight Sparkle, My Little Pony: Friendship is Magic, Original Character
Length: 17063

Cross over between Doctor Who and Mlp. (Some parts of this story connects with a story i wrote previous to this one. Is not published, and cannot publish it because i lost the first note book. Hope you can still follow along)

Doctor Whooves is living with Derpy and Dinky in his new house, in the middle of the Everfree Forest. He is in the middle of studying to find the cause for the strange things that have been happening. Shortly after moving into the forest, Princess Celestia sends three agents to try and kill Doctor Whooves and his family. He flees in his Tardis to find the Daleks minutes away from destroying Equestria and the rest of the universe.

It is up to Doctor Whooves and his friends to stop the Daleks and to convince Princess Celestia to keep him and family alive.

I will need help with grammar (not my strong point) if someone can help me with the grammar. I will be thankful. Message me here. If you suggest another place for contact let me know.Will also need help with detail. I'm ok with dialog but narrating is not my strength either

Published 2013-07-21 03:00:02 UTC
Last updated 2013-07-25 21:36:05 UTC

Everfree Forest

It's been three years since the war has ended. Doctor Whooves, Derpy, and Dinky have been living in their house in the Everfree Forest. Doctor Whooves has been studying the wild life in the forest, different from what he was used to doing, gave him a challenge which he likes. The animals in the Everfree Forest act differently compared to all the other animals in Equestria. Some of the creatures look very similar to the creatures outside of the Everfree Forest. Doctor Whooves captured a small rat and kept it in a glass container; examining  its every move. The was vicious, different from the other rats he has seen.

Doctor Whooves took a seringe and drew blood from both a regular rat and the rat from the forest. The Doctor took a look at the blood under the microscope to find that the cells of both rats are a bit different.

"Derpy, come take a look at this!" Doctor Whooves shouted through the house.

"What is it?" Derpy shouted back.

"I discovered something. Just come take a look."

Derpy walked down to the basement and took a look at the Doctor. "What is it?"

"The cells of these two rats are different." Doctor Whooves explained, "I mean they are the same in every aspect but one."

"And what is that one difference?" Derpy asked.

"There is a blue substance floating around the cells of the Everfree rat. Looks like aura, from a spell. It's not enough to say anything though. I'll have to take a look at the other cells and take samples of other species."

"Good luck" Derpy said.

Doctor Whooves went outside to see if he could capture a few different species. He grabbed a few plants on his tri as well, hoping that they'll have the same coating that the Everfree rat had. Doctor Whooves was just about to capture a rat, when The Doctor saw Twilight walking through the forest.

"Hey Twilight, that you?" Doctor Whooves shouted.

"Thank Celestia i found you." Twilight said.

"I've been living here for years." Doctor Whooves reminded, "Looks like somepony missed us."

"Doctor, this is serious."

"I think i figured out why the strange things in the Everfree has been happening." Doctor Whooves announced ignoring Twilight's concern.

"Doctor!!!" Twilight yelled.

"What?" Doctor Whooves complained, "Don't need to blow out my eardrums."

"You and your family are in danger."

"What do you mean?"

"Princess Celestia has hired three ponies to hung you and Derpy down, and kill you two."

"Whoa whoa whoa." Doctor Whooves interrupted, "When you say Princess, you mean our former leader that placed you in charge."

"Yes!!"

"What about my daughter?"

"I'm not sure, but pack your things and get out of this forest."

"I can't leave, I almost discovered the truth behind the Everfree Forest. Three years of hard work."

"It's either that or your family."

"This could save any lost traveler who ventures off into this forest."

"Doctor, listen to me. Princess Celestia has hired highly trained agents to hunt and kill you. Please, for your family's sake."

"Can you have somebody watch over this place while I'm gone?" Doctor Whooves asked.

"Sure thing." Twilight responded.

"How do you plan on solving this issue?"

"The only thing I can do is talk to her. She might kill me, but I'll do what I can."

"I need you to come to my house real quick.

"Something that only two ponies in this universe knows about. Derpy and Dinky, soon you.

The Tardis

"Right this way Twilight." Doctor Whooves guided as he opened up the door.

"It's just a blue box." Twilight Stated.

"Typical, every species say the same thing at first glance, but wait until you see what's inside."

"What's inside?"

"Why don't you come inside and see." Doctor Whooves said walking into the Tardis.

Twilight followed The Doctor into The Tardis. Her jaw dropped as she walked in. She ran outside to check all corners of the box, looking to see if she missed anything that could explain how the inside of the box is bigger than the outside.

"This is impossible." Twilight said

"Don't worry Twilight. That's how I reacted when I first saw the inside." Derpy said.

"This isn't possible."

"Trust me Twilight, nothing is impossible." Doctor Whooves said.

"Well I guess so, I mean my future self did go back in time to talk to me. I ended up doing the same thing.

"This Tardis can travel through time and space. And occasionally she likes to go where she pleases. Sometimes she crosses different universes."

"She?" Twilight questioned.

"My Tardis."  Doctor Whooves answered.

"It's a machine."

"And that's where you are wrong. The Tardis is a living creature. She has a heart and a life span. Even a soul. Just like any other creature. Did you know that stars are living creatures as well."

"Really?"

"Yup. I just learned that a few years ago. Anyways, I've been stuck on this planet for years now and who would've guessed that the Everfree forest would have something to bring my Tardis back to life."

"What fixed it?" Twilight asked.

"That purple plant that gave you and your friends weird symptoms that you thought was a curse. There's a substance there's a substance with in the flower that can fix various materials that i possess." Doctor Whooves answered, "By the way, what did you say about traveling back in time?"

"I went back in time to tell myself something, why do you ask. Still can't believe I went back in time."

"YOU WHAT!!!" Doctor Whooves shouted.

"What's wrong?" Derpy questioned.

"How long ago was this."

"Years ago. Maybe a week before the wedding with my brother and Cadence." Twilight answered looking confuesed

"Have you experienced anything strange. Ponies disappearing, creatures that you have never seen before that look like out of this world. Anything strange?"

"No, why what's the matter?"

"How long was your encounter?"

"A minute, maybe two."

"Did you make any physical contact. Shaking a hoof, hug, hoof bump, even  a simple nudge?"

"Not that i can remember."

"You're lucky?" Doctor Whooves sighed.

"How so?" Twilight questioned.

"Your universe could have been destroyed."

"Well enough with this time talk, you need to pack up and leave this part of Equestria." Twilight ordered.

"What's wrong?" Derpy asked.

"Princess Celestia has gone crazy. She has hired three Agent ponies to hunt and kill you two, she didn't mention anything about your daughter. Princess Celestia sent me to bring you to her, but I can't do that. Not after what you've done for us." Twilight explained, "Pack up your things and run."

"Derpy, I need you to grab Dinky. I'll get some food and other necessities."

"Yes Doctor." Derpy replied.

"Twilight, please look after this place for me." Doctor Whooves pleaded.

"Will do." Twilight said, "Stay safe."

Doctor Whooves nodded then ran to the kitchen and grabbed any food that he knew wouldn't spoil in a few days. He grabbed a cooler and threw anything he could into it. Meanwhile upstairs Derpy is trying to convince Dinky to leave the house, who is not budging.

"Derpy, What's taking you?" Doctor Whooves shouted.

"I'm trying to get Dinky, but she wont come out." Derpy answered.

"I'll be right there. Twilight can you put the cooler into the Tardis?" Doctor Whooves requested.

"Sure thing." Twilight responded.

Doctor Whooves ran up the stairs to Dinky's room, "What's wrong Dinky?" Doctor Whooves asked.

"I don't want to go into the blue box." Dinky cried

"We have too, there are bad ponies coming here and they will do bad things."

"Like what?"

"They will take Your mother and I away from you."

"What will the blue box do?"

"The blue box will make sure that we are all safe. It will take us away from those bad ponies, I promise."

"Will we come back?"

"Eventually yes, but first we need to make sure that the bad ponies will stop following us."

"Open up!" Somepony shouted while banging on the door.

"Derpy, grab Dinky and take her too the Tardis. I'll make sure that they don't get you." Doctor Whooves whispered.

Derpy grabbed Dinky and ran to the Tardis as fast as she could. Doctor Whooves followed right behind her and closed the door.

"Wait" Doctor Whooves shouted, "My Sonic Screw Driver. I'll be right back."

"We can do this the easy way or the hard way." The voice shouted again, "Guys stock up."

Doctor Whooves grabbed the Sonic Screw Driver from his room and ran to the Tardis. The three ponies kicked the door open. One of the stallions threw a small dagger at Doctor Whooves, but missed.

"Get him!" The leader shouted, "I will not disappoint the Princess."

Doctor Whooves ran to the basement where The Tardis is located. One of the stallions threw another dagger, hitting Doctor Whooves in the shoulder as he ran down the stairs. Doctor Whooves stumbled from the pain, but he wasn't going to let the affect him. Doctor Whooves noticed Twilight, hiding, trying not to be seen by the Agents.

"Twilight, in here." Doctor Whooves whispered.

"I can't Princess Celestia will kill me." Twilight argued.

"Not if she doesn't find out. These guys will kill you if they find out that you're working for me. I'm sure Princess Celestia could reason with you if you make it out of here with me."

"Fine, but where we headed." Twilight asked.

"Ponyville, now hurry inside." Doctor Whooves said running to The Tardis with Twilight right behind him.

"What happened to your shoulder?" Derpy questioned.

"Can't talk now, we gotta get out of here." Doctor Whooves said closing the door to the Tardis.

Doctor Whooves started to mess with the control panel to The Tardis, when the three agents started to bang on the door.

"Open up!" The leader shouted

"I'd rather not." Doctor Whooves replied as he pressed the last button, causing a strange noise to occur, "Well here we are."

Doctor Whooves opened the Tardis door to let his friends take a look. Everypony looked at The Doctor with confusion. Twilight walked out of The Tardis and nearly fainted when she realized that she was back in her old town.

"Did you put a spell on this thing?" Twilight questioned.

"Nope, this was made by my species, the time lords." Doctor Whooves explained, "It's not impossible. To a more important question. WHAT WAS THAT ABOUT!?!"

"Which part?"

"Well gee, I don't know. Maybe the part where my home was invaded and the part that I was almost killed!" Doctor Whooves yelled pulling the dagger out of his shoulder, "Derpy, bring me the first-aid kit."

"Yes Doctor." Derpy replied as she went to The Tardis to grab the first-aid kit.

"Patch up my wound please." Doctor Whooves ordered, "Why does Princess Celestia want me dead?"

"I'm not sure." Twilight responed

"There must be a reason. Did I do something illegal, is it the fact that I'm living in the Everfree Forest?

"No, it's more important than that."

"OUCH!!" Doctor Whooves yelled.

"Huh?" Twilight questioned.

"Sorry, it's the antibacterial spray." Derpy said

"Warn me next time, please."

"TWILIGHT!!!" A familiar voice shouted, running through tackling Twilight to the ground.

"Pinkie!" Twilight complained

"Hehe, sorry."Pinkie Pie laughed, "I thought you weren't coming down until Hearths Warming's Eve. Oh no... You lost track of time, didn't you. Well it's the middle of summer right now. I mean how can you not know, it's burning up right now."

"Pinkie I know it's summer, and I know it's not Hearths Warming's Eve." Twilight assured.

"Then why are you here silly?"

"Princess Celestia has hired me and three other ponies to hunt and kill The Doctor and his family."

"WHAT... IS SHE LOCO IN THE COCO!"

"I don't know Pinkie. We just came here for a few supplies." Doctor Whooves answered.

"Speaking of which, here's 20,000 bits." Twilight offered, "This should get you a decent house and get you some food for where ever you travel."

"Are you sure you want to give me this money? And why do you carry around 20,000 bits with you."

"Yes I'm sure, and I brought this 20,000 bits specifically for you. Besides i get plenty of money. It's not like I need it, but being royalty, you tend to get a lot of it. I just give it to ponies who need it more than me. In this case you are one of those ponies."

"Thanks Twilight."

"Don't worry about food." Pinkie Pie said, "I'll go get you some cupcakes and other goods from the Sugar Cube Corner"

"Thanks Pinkie. Twilight can you do me a favor?" Doctor Whooves asked.

"What is it?" Twilight answered.

"I need you to make sure that The Tardis doesn't leave Ponyville."

"Why are we leaving the Tardis?" Derpy asked.

"We can't be have Ponies seeing it. It'll give us away."

"How so?"

"Think about it, a blue box appearing out of nowhere. How weird would that be?"

"But ponies know about what you have done for Equestria. You are the reason why Equestria is still alive." Derpy argued.

"With Celestia in power, she can make ponies believe anything." Doctor Whooves informed.

"But Twilight is the new leader."

"Celestia is a role model to ponies all over Equestria. Whether she's in power or not."

"To be honest, Princess Celestia has only made me leader of certain things in Equestria." Twilight added, "She still controls the land and she over powers me. If I do something she doesn't like then she can fix it the way she'd like it."

"So, technically she's in power still." Doctor Whooves assumed.

"Correct. She just needs somepony to look after Equestria while she's at the Crystal Empire."

"Can't she give somepony the power to activate the heart?" Derpy asked

"I'm sure she could, but the only ponies she can fully trust are Cadence, Luna, and me. I'm too weak, Princess Cadence is dead. And, well, Princess Luna is easily persuaded and is busy looking after everpony in their dreams."

"Makes sense to me." Doctor Whooves said, "But if she's all the way at the Crystal Empire, how do we reason with her?"

"We?" Twilight jumped, "if she sees you, she'll have all her guards kill you and Derpy."

"There must be something that we can do."

"There is, and that's getting out of this town."

"Where do we go?" Derpy asked.

"Anywhere, other than Canterlot, Ponyville, The Crystal Empire, or your house. I recommend taking this box. You'll be safer with it."

"Understood Twilight. How is the wound coming along Derpy?"

"It's not too bad. The blade didn't cut any muscles or anything important, just skin and flesh. Should be fine with in a few days." Derpy informed.

"Good. Now get in The Tardis. I'll be right with you."

"Okay Doctor." Derpy said hopping into The Tardis.

"Thank you Twilight."

"You're welcome Doctor. Hopefully I can talk some sense into Princess Celestia."

"Bye Twilight." Doctor Whooves said walking into the Tardis.

"Where is our next destination?" Derpy asked.

"Appleloosa." Doctor Whooves replied.

Doctor Whooves looked through the camera to see Twilight walking away from The Tardis. He waited a little while before setting the coordinates on The Tardis. "See you soon" Doctor Whooves whispered to himself before pressing the last button to Appleloosa."

"WAIT!!!" Pinkie shouted running towards The Tardis with a basket full of muffins and cupcakes.

"Pinkie, he left." Twilight informed.

"But, they forgot their food."

"Don't worry pinkie, they'll be back."

"I hope so...... Hey would you like to come to my party?" Pinkie Pie asked.

"I'd love to. It'd help get rid of some of this stress." Twilight responed.

"Good, get Applejack, Fluttershy, and Rainbow Dash."

Agent Leon

"Enter, Twilight." Princess Celestia ordered.

"Yes, your majesty." Twilight called back.

"I've been thinking about this for the past few years and I have finally came up with and answer. I need the four of you to find and kill both Doctor Whooves and Derpy. Don't disappoint me."

"I thought you were going to let them live." Twilight shouted.

"I'm sorry Twilight, but it must be done."

"Yes, Princess."

"You leave tomorrow morning. Twilight, I need you to lead my agents to the Doctor's house. Now leave this room."

"Finally, some action around here." One of the agents spoke while leaving the palace.

"I know, I'm tired of paper work and worrying about petty crimes." The other Agent agreed.

"I hope you know that this isn't going to be fun and games." The last agent informed.

"How would you know. You've never been on a mission like this." The first agent argued.

"You're right. I've been in far worse situations than this."

"What trouble can a colt like you possibly get involved with?"

"Let's see, I defended Canterlot during the changeling attack. I escaped from this facility, which I was the only pony to do so before it got shut down. Also I fought front lines in the war that ended a few years ago."

"Who are you?" The first agent asked.

"My name's Agent Leon." Agent Leon replied.

"West."  The agent spoke again.

"Good to know, what about you ma'am?"

"Tanya." The last agent answered.

"Good, now that we know each other's name, we can move on." Agent Leon said, "Now head to the barracks and rest. Hopefully we can get this mission done by 10:00 o'clock dusk tomorrow."

The three agent went to the barracks and rested. They ate food, drank wine and cider and did what ever they could to keep themselves occupied until they had to sleep. Agent Leon on the other hand studied his mission in and out to discover that Doctor Whooves is an alien species from a different universe.

:"Good thing I read up on the mission. Last thing I need is some laser shooting at us by surprise." Agent Leon thought to himself. "Hmm, It's nine o'clock already. Better catch some sleep.

"Everypony head to bed." Agent Leon ordered.

"It's only nine o'clock." West argued.

"And I don't want to carry you to the mission. We are getting up early as well. I don't want to spend my whole day doing after one pony. So go to sleep."

"Everypony went to bed that night. Agent Leon slept on a couch in the living room while Tanya and West slept in separate rooms upstairs. The sun was shining through a window onto Agent Leon's face. Agent Leon woke up looking at his clock seeing that it's eight o'clock.

"Shoot!" Agent Leon tried to shout, "Everypony get up!" He shouted.

"It's only eight in the morning." West complained.

"We are supposed to to be there in two hours. Tanya, are you up?"

"Ready to go sir." Tanya responded

"C'mon West, get ready. We're leaving in 10 minutes." Agent Leon informed.

"Who made you in charge?" West argued,

"Princess Celestia did. If you have a problem with that then take it to her."

"Question, how are we supposed to find the Doctor in two hours?" Tanya asked.

"Simple, we get Twilight to teleport us." Leon responded.

"Where is she?"

"She's in the same Palace Princess Celestia is living in."

The agents walked to the Palace to get Twilight. At the main entrance, guards with spears sat at the gate, waiting for trouble. The guards shifted the spears towards the Agents.

"State you business." The guard ordered.

"We are here to speak to Twilight Sparkle." Agent Leon answered.

"Why should we let you in?"

"We are on a mission given by Princess Celestia. That's all the information that I can give you."

"You're allowed in." The guard said, giving Agent Leon a stare, "Don't cause any trouble."

"Yes sir."

Agent Leon and his fellow agents went to Twilight's room and knocked on the door. It took a little while for Twilight to answer due to studies, but she finally answered the door.

"Hello, um...." Twilight said uncertain.

"Leon." Agent Len responded.

"Oh... right, what do you need?"

"I need you to teleport us to the Everfree Forest."

"I can't teleport you to your exact destination, but I'll try to get you as close to it as I can." Twilight offered.

"That'll work." Agent Leon accepted.

"Spike."

"Yes, Twilight?" Spike answered.

"Stay here and don't touch anything." Twilight commanded.

"Okay, fine."

"I'll see you in a few hours Spike." Twilight informed while casting her teleportation spell.

Twilight purposely teleported at the edge of the Everfree Forest, so she could have more time to think of a plan to warn Doctor Whooves. The scenery for the agents was outstanding. Neither one of them have been this close to the Everfree Forest.

"This place is beautiful." Tanya spoke out.

"Don't be fooled by its appearance." Twilight warned, "The Everfree Forest is the most dangerous place in Equestria."

"It's nothing we can't handle." West boasted.

"Shut up!" Leon groaned, "And don't do anything stupid"

"Leon, Tanya, and West followed Twilight through the forest. They saw creatures that they have never seen before, both normal and abnormal. Alligators, jaguars, and wolves. One of the creatures Twilight warned them about, is the timber wolf. There is no absolute way to kill these creatures, other than fire. West started boasting and said he could take on anything. Agent Leon just thumped him on the back of his head.

"Okay guys. Wait right here." Twilight ordered, "I'll go to The Doctor's house and take care of this on my own. Don't follow me, unless I call for your help."

"Yes, your majesty." Agent Leon said as Twilight walked away.

30 minutes later.

"What's taking her so long. All she has to do is shoot the two with her magic." West complained.

"C'mon Leon." Tanya said, "She might be in trouble."

"Okay, we'll go. But only to shut you two up. Follow me." Agent Leon said.

Agent Leon followed Twilight's tracks that she left in the wet ground. He followed them until he found the house that Twilight was looking for. He walked up to the house and heard voices. He put his ear to the door to listen in on the conversation. Agent Leon could hear the voices, but he couldn't make out what they were saying.

"West, Tanya, Stalk up at the door." Agent Leon ordered.

"Yes sir." Tanya said, moving into position.

Agent Leon knocked on the door hoping for an easy kill, "Open up!" Agent Leon shouted. He waited a few seconds before he spoke again, "We can do this the easy way or the hard way!" He shouted again. Agent Leon kicked the door in and spotted Doctor Whooves, "West, Tanya, go after The Doctor. I'll find his wife."

"West grabbed a dagger from his coat and threw it towards Doctor Whooves but missed. West threw another blade and hit Doctor Whooves in the shoulder.

"She's down stairs!" Leon shouted, "Run after them!"

"Leon and the other two ran down the stairs to Doctor Whooves. Leon saw Doctor Whooves and Twilight enter The Tardis. He ran towards the door and tried bucking it in, but the door did not give in. The blue box started to make a strange noise. Agent Leon looked up in surprise when he saw the blue box disappear.

"Damn!" Leon shouted, "HE WAS IN OUR GRASP, HOW DID YOU LET HIM GET AWAY!!!"

"I MISSED WITH MY DAGGER!" West shouted in defense.

"He wasn't even 10 feet away from you! How did I get paired up with you two."

"Look what I found." Tanya said, "It's some type of metallic device. It has a place for your hoof. Wonder what it does." Tanya said placing her hoof in the slot with a loud  bang following.

"What was that!" West shouted.

"It's a gun." Agent Leon said, "It's used to kill ponies. So I'd put it down, before you hurt somepony. Lets look around for other things that may be mysterious."

"What about Twilight?" West asked, "We got save her."

"She's a traitor. She wasn't kidnapped, she when with The Doctor willingly." Leon responded, "We must report back to Celestia. Tanya, West, look around for anything that may be useful to us, or harmful to us. I'm going to Ponyville to take a train back to The Crystal Empire. And what ever you do... DON'T PLAY WITH ANYTHING!!!."

Traitor

Agent Tanya and Agent West have found a way to contact Princess Celestia with one of the devices in the house. They just happened to touch it and it turned on.

"Enter a Location." The device said.

"Um..." West said unsure of what to say.

"Location not found. You must enter location and name to contact the person you are trying to reach." The device said again.

"Crystal Empire." West said.

"Crystal Empire acquired. Now enter name."

"Princess Celestia." West spoke out.

"Princess Celestia contacted. Please wait...... You are now connected to Princess Celestia."

"Princess Celestia, can you hear us." Tanya called out.

"Yes, I thought you were going to get rid of Doctor Whooves and Derpy. Why are you back so early?" Princess Celestia questioned.

"We are still in the Everfree Forest. We are still in The Doctor's house. We have found this device that connected the two of us to you." West informed.

"Did you kill them?"

"No we did not. They got away."

"WHAT YOU LET THEM GET AWAY!" Princess Celestia shouted.

"Yea, but we have important information." Tanya said.

"What is it?" Princess Celestia questioned .

"Twilight has betrayed us."

"What makes you say that."

"She escaped with The Doctor. She walked into the blue box with him, before it disappeared."

"Are you sure she wasn't kidnapped?"

"I am positive. She ran with him."

"That's unfortunate." Princess Celestia whispered to herself.

"What would you like us to do?" West asked.

"I want you to go to Ponyville and hang around there. Wait for Twilight to show up. Once you spot her, take her in for questioning." Princess Celestia ordered.

"What happens after that."

"Whether she is being cooperative or not, I want you to kill her when you are done interrogating her."

"It will be done." Tanya said.

"Don't disappoint me again. If you do, I'll have you both executed."

"Yes your majesty."

"Don't speak to me until the job is done." Princess Celestia ordered.

"You have 30 seconds left before this connection shuts down." The device said.

"Well that didn't go too bad" West said.

"What are you talking about. Our heads are on the line right now." Tanya argued, "If we fail we will be killed by Celestia's hooves."

"I still can't believe she wants her own student dead though."

"She was just protecting her friends."

"Do we even know why we have to kill The Doctor?" West questioned

"Apparently he's an alien species. I did believe it until now."

"Well, that's good enough for me." West said, "Come on, lets go. We must find Twilight. Before Princess Celestia decides to send her guards after us."

"Yea good idea." Tanya agreed.

"This system is now shutting down." The device said, "Thank you for choosing this company."

Agent Tanya and Agent West left The Doctor's house shortly after the brief encounter with Princess Celestia. The two agents have been walking around The Everfree Forest for a few minutes before spotting Agent Leon off in the distance.

"Agent Leon is that you?" West shouted.

"Just ignore them, just ignore them." Agent Leon whispered himself.

"Agent Leon hold up." West shouted once more.

"What is it?" Agent Leon groaned, "I thought I told you to stay in the house."

"You did but we got message from Princess Celestia." West informed.

"She wants us to capture Twilight. Ask her questions about The Doctor, and then kill her." Tanya added.

"How did you two manage to get a hold of Celestia." Agent Leon questioned.

"Long story." Tanya said, "But she wants us to stay and wait in Ponyville and wait for Twilight to show up."

"That's not a bad Idea. The Doctor probably left Twilight there to keep her safe. And if she's there, than The Doctor and his wife must be too."

"We may be there for a while." West said.

"That doesn't matter, I'm sure we can find somepony who will be more than glad to stay with them. Maybe even a free hotel with free food."

It took the three agents about two hours before getting out of the forest and another hour to walk all the way to midtown Ponyville. After hours of walking around the town, they have finally found a hotel that's willing to let them a few nights for free. Agent West walked into the room and fell onto the bed and just laid there."

"You see. This is good customer service." West said with his face buried into the mattress, "Nice comfy bed, comfy pillows, even a shower."

"Our Baracks had an oven." Tanya said bluntly, "Along with all this other stuff."

"Hey, it's better than sleeping in the dirt."

"We still have job guys. We can rest for today, but tomorrow early we have to stakeout this area. We stay in this hotel, and we all have shifts. Two hours and switch. We'll do that until we find Twilight." Agent Leon ordered.

"Sound good to me." West said.

"Is it alright if I head to a bar?" Tanya asked.

"Sure, but don't let Twilight, Derpy, or The Doctor see you before you see them" Agent Leon said

"I won't" Tanya sighed.

"And for Celestia's sake, don't get wasted."

"Okay father I won't." Tanya said sarcastically, "West, want to come with."

"No thank you." West replied, "But can you bring me back a bottle of Applejack Daniel's"

"No promises."

Tanya walked out of the hotel and spotted a bar just a little bit down the street. She walked down a little bit and saw one of Twilight's friends. She didn't remember the name. She thought about asking the Pink mare, but decided against it. "It's too late right now. I'm sure that pink mare will still be here tomorrow." Tanya continued her way to the bar and finally walked it.

"May I take your order?" The white mare asked.

"Just some wine." Tanya replied.

"Anything food?"

"No thank you."

"HEY OCTI WINE OVER AT TABLE FIVE." The white mare shouted.

"Wait.. Aren't you Vinyl.

"Yup, the one and only. How'd you guess."

"I just remember you somewhere. Didn't you own a bar up in Canterlot."

"Yea we did, but since the attack with King Sombra towards the end of the war three years ago, we had to close down. The expenses in Canterlot skyrocketed. With the building being destroyed. We decided to come down to Ponyville. More relaxing. And the building doesn't cost as much to maintain."

"I'm sorry to hear. Well have a good night Vinyl."

"You too Ma'am." Vinyl Scratch said.

"You can call me Tanya."

"Well Tanya, Octavia is here with your drink. Enjoy.

Tanya walked over to her booth and started to sip on her wine. Looking around at the bar scenery. While keeping a look out for Twilight as well. Tanya laid her head on the table trying to relax a little bit. Before she was rudely interrupted.

"Hey there cutie."

"West I swear to the nights, I will punch you if you don't leave me alone." Tanya groaned.

"How do you not recognize my voice."

"Because I can care less West. Just please let me rest

"It was a pity to hear that. Well I'm a Pegasi guard My name's Lace" He announced.

"Yea sorry. Not interested." Tanya said turning her head away.

"How can you not be interested in me? Im a guard."

"Yea and I'm an agent."

"Which is exactly why I came here. Princess Celestia wanted me to remind you to get the job done."

"Yes I know."

"If you don't capture Twilight by tomorrow at dusk, then I will kill you. But I can let you loose if you do me a favor."

"You can forget about it." Tanya said sipping her wine, "Now let me enjoy my peace."

"Why don't I help you." Lace grinned as he sat down next to Tanya.

"I will give you three seconds to get away from me." Tanya growled.

"Or what." Lace said putting his arm around Tanya.

Tanya quickly moved under his arm and knocked the colt onto the ground, with his hoof in a painful position. She applied a little but more pressure enough tear a muscle in his arm.

" I warned you." Tanya whispered in his ear before spitting on him.

"Is there something wrong?" Vinyl Scratch called out quickly running towards Tanya.

"He'll be fine. Hey, can I get two bottles of wine, and a bottle of Applejack's to go."

"OCTAVIA, TWO BOTTLES OF WINE AND A BOTTLE OF APPLEJACK DANIEL'S AT TABLE FIVE!"

"OKAY BE RIGHT THERE!" Octavia shouted back.

"Seriously though, what did you do."

"I did my job." Tanya said pulling out a few bits to pay for the three bottles, "Catch you some time later. And sir, I recommend leaving me alone for now on. Consider this your final warning."

Tanya walked back to the hotel and pulled out the drinks from her bag.

"What took you so long?" West questioned, "Had to deal with business. I got a bottle of Applejack for you. and Wine for you Leon."

"Well we can't stay up too much longer. We have to be functional tomorrow if we want to catch Twilight." Agent Leon suggested. Good night."

Agent Leon woke up early that morning and started to look out the Window. He could see fillies and colts playing outside, mares shopping around. And the Stallions going to work. Agent Leon wasn't concerned about that though. Agent Leon could see Pinkie Pie walking around with food. I stared at her, wondering if she was one of Twilight's friends or not.

"I better go question her. I bet she'd know where Twilight is." Agent Leon thought to himself, "West, Tanya get up. I'm going outside to ask this pink mare a few questions. I will be back in roughly five minutes.

"yea yea." West moaned.

"Or I'll wake you up when I get back." Agent Leon grunted.

Agent Leon walked outside and spotted Pinkie Pie and was about to walk up to her when Pinkie Pie ran up to him.

"Hey my name's Pinkie Pie you must be new here in Ponyville, because I haven't seen you around and I know everpony in Ponyville but not you so that must mean you're here. What's your name. My name's Pinkie Pie, I think I already told you though, but just in case you forgot." Pinkie Pie said in a mouthful

"My name is Leon, Have you...."

"Hello Leon, nice to meet you. Do you have any friends here, are you visiting or are you moving in. Ooh let my guys your a tourist. No no, we never got those here. Ooh you're a photographer. I can tell by your outfit and sunglasses.You know. So you don't have to worry about the sun when taking a Picture of the sky. Ooh have you ever had any of my...."

"Shut up!" Leon yelled, "I am here to ask you a few questions. After I ask these few questions I don't want to be bothered by you. Got it?

"I understand." Pinkie Pie frowned, "You don't want to be bothered. Just like Cranky Doodle Donkey. But that's ok. I can still be your friend."

"Have you seen Twilight?"

"Last time I saw her, she was with The Doctor and Derpy. Twilight is still in town. But The Doctor and Derpy went somewhere else. I don't really know where though. Apparently Princess Celestia wants them captured. I think they are just playing though. Because Twilight is Princess Celestia's number one student. I think Twilight is at the library.  She walked with me half way to the Sugar Cube Corner, then she said she had some studies to get too."

"Thank you."

"Oh by the way, as a tradition of Ponyville. I would like to invite you to a party. I was going to throw one anyways. But this is a perfect opportunity to get some new friends." Pinkie Pie offered.

"Sorry, but I have to decline that invitation. I am on a job given by Princess Celestia." Agent Leon informed.

"Ok well if you change your mind, meet me at Sugar Cube Corner later tonight. six o'clock maybe."

"We'll see. Maybe we'll see each other again."

"Ok, Say hello to Twilight when you catch her."

"Will do." Agent Leon said, walking back to his hotel, "West, Tanya we have a lead."

"Huh." West said just starting to wake up."

"We have a lead on Twilight. Get up. Her friend Pinkie Pie that Twilight is at the library."

"About time." Tanya said walking out of the shower.

"You're up already?" Leon questioned.

"I know when there's a job to do." Tanya stated, "And I can get myself up if I need to, which in this case I needed too, West on the other hoof, is just a lazy bum and just wants to sleep all day."

"Hey I am not lazy. I'm just a very relaxed pony."

"So that's what they call nowadays. Gotcha."

"Well we need to get going, before Twilight changes her location." Agent Leon ordered, "We don't have much time."

"Oh speaking of time. Last night, this guard came up to me and told me that we have until the end of the day to get rid of Twilight. She has sent guards to execute us if we don't." Tanya mentioned.

"And you didn't care to tell us this before now?"

"Hey I was pissed and tired. It slipped my mind."

"Anyways, lets go."

"Let me get shower." West said.

Leon grabbed the bottle of wine from last night and poured it on West. "The alcohol will kill what ever bacteria you have on you. Now get up."

West got up from bed and grabbed a towel to wipe his face. Tanya and Leon walked out of the hotel and headed towards Twilight's library. West ran to catch up to the other two agents. As they got closer to Twilight's library, they could see Twilight reading some books through the window.

"There she is." Agent Leon whispered, "Tanya you go check for a back door. West you look for a side door. I will knock on the front door. I'll give her 10 seconds before I kick down the door."

"Understood sir." Tanya said.

Agent Leon knocked on the door waiting for somepony to answer the door, "Be there in a minute." Twilight shouted. Agent Leon knocked again. A few more seconds he kicked down the door. Agent Leon walked up stairs and spotted Twilight who was startled.

"You know the door was unlocked, right!?" Twilight yelled, "Now I have to get that fixed."

"Come with me Twilight." Agent Leon ordered.

"Why what's wrong?" Twilight questioned.

"I know you know just as much as I do." Leon said.

Leon walked Twilight down the stairs before Twilight bucked him. West and Tanya heard some crash inside the library and quickly entered the building. West ran after Twilight who tried to flee the building, while Tanya went to check up on Leon.

"Don't worry about me." Leon said, "Get Twilight."

West tackled Twilight down and put cuffs on her.

"Let me go!" Twilight shouted.

"You come with us quietly and this'll be easy. We just need to ask you a couple of questions." West said, "I will uncuff you if take us to a closed space for us to speak without any interruptions."

"There's a warehouse that we can talk. Nopony goes there often. I can take you there."

"That'll work" Agent Leon agreed, "Take us there and don't do anything stupid. There's three of us, and one of you."

"I won't, just follow me."

Twilight led the agents to the warehouse she was talking about. The warehouse was full of boxes and rusted metal. West pulled out a rope but Leon signaled him to put it away. Twilight went to another room that belonged to an old business called 'Sofa and quills'. The place was dimly lit. With two low lighting hanging lamps in the room.

"Tanya, West, you two stay here. I'm going to walk around outside." Agent Leon informed, "Ask her anything that'll get us closer to The Doctor and his wife." He whispered in Tanya's ear

"Understood." Tanya replied as Agent Leon walked out, "West get out the rope."

"So you don't try to attack us." West said pulling out a rusty chair.

West tied up Twilight to the chair, for some reason she didn't fight back which made it very easy for West.

"We are going to ask you a few questions. Answer truthfully." Tanya said, "First question, why did you go with The Doctor?

"He is a good friend. Native to this planet or not. He helped me in many different ways. I was going to stay in the house, but he told me that you wouldn't be to happy with me."

"Why did you help him out?" West interrogated.

"Like I said, he's a good friend. I couldn't let him be killed. Not under my hoof. He saved Equestria, whether you want to admit it or not. He found the week points. He was able to warn us and tell us what must be done, in order to save Equestria. He's also trying to find a way to save ponies from the Everfree Forest. He has helped us way too much to let that all fade away."

"I'm sure Princess Celestia has a valid reason for wanting him deceased." Tanya assured.

"She's probably scared that he'll take his spot!" Twilight shouted, "That is not a valid reason."

"Anyways. Last question, Where is the Doctor."

"Right here!" Agent Leon said pulling in The Doctors body.

"HE BETTER NOT BE HURT!"

"Shut up." West said hitting Twilight hard enough in the head to knock her out.

Devastation in Appleloosa

Few hours before the capture of Twilight and Doctor Whooves

"Here we are." Doctor Whooves said opening The Tardis door, "Appleloo....... Oh my" Doctor Whooves said

Doctor Whooves' jaw dropped when his eyes registered what he was looking at. There were piles of skeletons everywhere, with huge pot holes in the ground and burn marks all over the place.

"What happened?" Derpy asked covering Dinky's eye, "I thought they were going to turn this place into a memorial.

"They did." Doctor Whooves said, "Looks like this place was attacked. Both changeling and pony skeletons. Looks like dragons have attacked. There are burn marks on the bones and houses."

Doctor Whooves walked to one of the skeletons to see if the body was still warm. He touched the skull, it was still warm to the touch. Doctor Whooves stood up and looked for any signs for the dragon or dragons.

"Derpy, we must leave." Doctor Whooves said, "There are dragons nearby. I'm sure of it"

"Shouldn't we check for survivors. There must be at least one pony alive somewhere here." Derpy suggested.

"Okay, you check the housed, I'll check the stores and restaurants."

"What about me daddy?" Dinky whined.

"You stay here and don't open The Tardis door for whatever reason. I have my Sonic Screw Driver, so I'll be able to get in." Doctor Whooves replied.

"What about mom?"

"She has a key. I'll be back in an hour, maximum."

"Stay safe hunny." Derpy called walking out of the Tardis.

Doctor Whooves searched the stores and restuarants for any signs of changeling or pony life. Doctor Whooves heard rattling in some of the houses, but it would only be a rat or a bug of some sort.

"Anypony here?" Doctor Whooves spoke at the salt bar. He waited a few seconds before giving another call. "This is your last chance. If you don't come out or speak, I'll leave without you.

Doctor Whooves walked out of the bar and saw Derpy walking out one of the houses. He ran up to Derpy giving Derpy a quick hug.

"Which houses have you checked?" Doctor Whooves asked.

"I've searched everyone of them." Derpy replied, "But not a soul in sight.

"Well, we better head back to The Tardis before that dragon gets hungry again." Doctor Whooves said right before he heard a roar of three dragons, "Speaking of the devil.... RUN!!!"

Doctor Whooves and Derpy ran to the nearest building they could find. They ran into the salt bar, which happened to be right behind Doctor Whooves.

"Well. Looks like we are stuck here for a little while." Doctor Whooves said.

"What about Dinky, She's stuck in the box." Derpy cried.

"Dinky is safe. She has food and water. And the dragons can't get her inside The Tardis."

"HELP!" A voice shouted from outside of the building.

"Derpy, stay here. I'm going after the voice."

"Be careful Doctor." Derpy said.

Doctor Whooves ran out of the building and saw a filly running away from the dragons. Doctor Whooves then ran towards the filly as fast as he could. One of the dragons swooped down and almost grabbed a hold of the filly. Doctor Whooves jumped towards the filly and tackled her out of the way. Doing this caused the dragon to grab Doctor Whooves instead.

"You better let me go." Doctor Whooves warned pulling out his Sonic Screw Driver, "This right here is a dangerous weapon. Don't make me use it."

"You let this happen to us. You have summoned them here. And we will make you pay." The dragon spoke.

"What are you talking about? I haven't done anything." Doctor Whooves argued.

"They are here for you." The dragon said letting go of The Doctor.

The Doctor fell through the roof of the salt bar. Derpy jumped out of the way and quickly ran towards him when she noticed that it was Doctor Whooves.

"Doctor, are you okay?" Derpy cried.

"Yea I've been through worse." Doctor Whooves groaned, "But boy, that hurt. I gotta go back out there for the filly."

"What about the dragons?" Derpy questioned

"Oh no worries, I think they flew away." Doctor Whooves said walking out of the bar.

When Doctor Whooves walked outside of the bar, he could see the filly sitting down on the side of the bar.

"Hey there, are you okay?" Doctor Whooves asked.

"Yea I'm fine." The light brown filly responded.

"Were these the dragons who attack you?"

"Yes, Who are you?"

"I'm The Doctor. Doctor Whooves works as well."

"Oh my gosh. You are the one who fought the war with Princess Celestia, Twilight, and my cousins."

"Who are your cousins?" Doctor Whooves asked

"Apple Bloom, Applejack, Brae Burn, and Big Mac." The filly responded.

"What's your name?"

"Babs." Babs responded

"You're alive?"

"Of course! Why wouldn't I be?"

"Princess Celestia has you among the deceased list. Sadly a few other ponies as well."

"Who are the other ponies?"

"Flim, Flam, Shining Armor, Princess Cadence, Big Machintosh, Granny Smith, Brae Burn, Rarity, Trixie, and Queen Chrysalis." Doctor Whooves responded.

"Oh my. How long ago was this?" Babs questioned.

"Rarity, Princess Cadence, Flim, and Flam died five to six years ago. The others died three years ago." Doctor Whooves informed.

"Can you take me to Sweet Apple Acres?" Babs asked trying to hold in her tears."

"Yea sure thing. Hey Derpy, lets head to the Tardis, the cost is clear."

"Okay Doctor." Derpy said walking out of the bar.

"Derpy!" Babs shouted giving Derpy a hug.

"You two know each other?" Doctor Whooves questioned.

"We saw each other at the parade all those years ago." Babs said.

"You were doing something in the lab back in our old house." Derpy added.

"Explains a bit. But no time to waste. We must take you back to Ponyville."

"Thank you Doctor." Babs said.

"You're welcome." Doctor Whooves said picking up Babs on his shoulders.

Doctor Whooves and Derpy took Babs to the Tardis. Doctor Whooves opened the door letting Babs down. Doctor Whooves followed Babs into The Tardis. Babs was surprised to see the inside of The Tardis.

"We won't be able to stay for long Babs" Doctor Whooves informed.

"Why is that?" Babs questioned

"Princess Celestia has hired a couple of goons to kill me." Doctor Whooves answered.

"What did you do?"

"I don't know. If I knew what I did wrong, I'd turn myself in. I guess Princess Celestia has gone mad. Although I'm getting a feeling it has to do with something that the dragon told me."

"What did he say to you?" Derpy questioned.

"They said it's my fault. I am the one who summoned them and that they are here for me. I have no idea what that could mean though. It doesn't matter, we are wasting time." Doctor Whooves said setting the coordinates to Ponyville.

"Here we are Babs." Doctor Whooves announced, "Welcome to Ponyville."

Babs took a step outside of The Tardis, confused, she looked around and came to the conclusion that she was in Ponyville.

"How did we get here?" Babs questioned.

"By using this machine. It's a teleporter and a time traveling machine. Well I really shouldn't call her a machine."

"Huh?" Babs questioned.

"The Tardis is a living creature. It's hard to explain. Anyways, let's get you to your family."

"Please do." Babs begged

"Derpy." Doctor Whooves called, "I need you and Dinky to stay here. If anything happens, use The Tardis and go anywhere off this planet." Doctor Whooves ordered.

"What about you?" Derpy questioned.

"I'll stay here in Equestria, hiding from Celestia."

"Okay, stay safe Doctor."

"I'll try Derpy. Are you ready babs?"

"Yes sir." Babs replied.

"C'mon, lets go."

Doctor Whooves led Babs to Sweet Apple Acres. The Doctor explained the issue to Babs about Princess Celestia, and everything about how he landed in Equestria. He talked about the Daleks, Cybermen, and other odd creatures he has seen in his travels.

"You have some strange stories." Babs commented.

"But they aren't stories." Doctor Whooves explained, "I really am a time traveler. My species are called time lords. I am the last of my kind. Maybe one day I can take you to see the universe."

"I'll pass. I just want to see my family."

"I understand. Sweet Apple Acres is just this way."

Doctor Whooves and Babs made it to the gate to Sweet Apple Acres. The Doctor waited at the gate allowing Babs to continue without him. Doctor Whooves watched as Applejack opened the door. Applejack's face dropped, giving  Babs a hug. Apple Bloom followed and gave Babs a hug as well. Doctor Whooves could only see the tears on their faces. He knew the tears were filled with both happiness and sadness. Doctor Whooves drew a tear thinking about his past.

"The last time lord in all of space and time, stuck here in this universe. I'm supposed to be out there, protecting the human race and all the other life forms, but instead I'm stuck here with a family. Thank you Tardis. What ever went wrong with you, I'm glad it did." Doctor Whooves thought to himself, "I'm finally free"

"Not for long." Somepony whispered, knocking Doctor Whooves in the head with a blunt object.

Discovery

Doctor Whooves woke up tied to a metal chair. His vision was blurry for a moment. He blinked a few times and his vision cleared up. he saw two stallions and a mare, talking to each other but wasn't able to make out what they were saying.

"Where am I?" Doctor Whooves questioned.

"Quiet!" One of the stallions commanded, "You're going to answer my questions. Don't lie and you'll be safe. But where are my manors. My name is Leon and these two are Tanya and West. Who are you."

"The Doctor," Doctor Whooves replied.

"Doctor Who?" Tanya questioned.

"Just The Doctor," Doctor Whooves insisted.

"Where are you from?" Agent Leon interrogated.

"A galaxy far from here," Doctor Whooves replied.

"Stop playing games," West commanding while hitting The Doctor.

"I am from Galifrey. It's destroyed!" Doctor Whooves cringed.

"What is your species called?" Agent Leon questioned

"I am a time lord. The time lord, the last time lord in all of existence," Doctor Whooves said.

"Now one more question. Where is Derpy?"

"I will not tell you."

"Oh but you will," Agent Leon said.

"What can you possibly do to me. I've been through far more pain than you could ever deal to me."

"Then we'll just have to kill your former companion. West bring Twilight in."

"Princess Celestia will have you executed!" Doctor Whooves shouted.

"Princess Celestia has ordered us to kill her as well. It's either Twilight or Derpy"

"How do I know that you wont kill her if I tell you where Derpy is?"

"What's a stallion without his honor? You can't have honor if you lie, now can you?"

"You're worried about honor, but you're willing to kill an innocent are with a little filly!" Doctor Whooves shouted.

"Doctor, don't tell them anything." Twilight moaned as West dragged her in.

"Shut your mouth traitor!" West hissed pushing Twilight to the ground.

"West, kill them both. Tanya, your going to help me find Derpy." Leon ordered.

"Yes sir." Tanya replied.

Agent Leon and Tanya left the building to search for Derpy. West grabbed a knife from the table and pointed the knife towards Doctor Whooves.

"Any last words?" West grinned as Twilight covered her eyes

"Actually... yes," Doctor Whooves chuckled, "Look out."

Agent West got hit with a shovel in the back of the head. West fell to the ground with an orange mare standing behind him.

"Applejack?" Twilight questioned.

"Just returning a favor," Applejack said undoing the restraints on The Doctor.

"It was nothing," Doctor Whooves insisted.

"But it's everything. You brought back family. Don't know about you, but that's everything a pony would wish for. And it's a debt that can never be fully repaid. Enough talk, we gotta get out of here."

"You bitch!" West shouted as he stabbed Applejack in the leg.

Applejack let out a loud yell, Agent Leon and Tanya heard it from outside the warehouse and quickly ran back to the room. Agent Leon entered the room to to find Twilight up and walking, Applejack laying on the ground, and Doctor Whooves attacking West.

"Tanya, after Twilight. The Doctor is mine," Agent Leon commanded.

"Twilight, hand me the Sonic Screw Driver!" Doctor Whooves yelled. "Applejack, you hang in there. I'll get you out of here."

"Doctor, catch!" Twilight shouted.

"Fantastic!" The Doctor shouted catching the screw driver, "Okay, I'll warn you once and only once. This screw driver is a weapon. It can kill you in a press of a button. Let us go and I'll let you live. If not, then I'll kill all three of you."

"What makes you think we will believe you. It's just a screw driver," Agent Leon taunted.

"Do you really want to take that chance. I mean I came to this town in a blue box. Which by the way is bigger on the inside than it is on the outside. I have two hearts. I've been living for hundreds of years. Oh this one is my favorite. I can travel through time and space, hence the term time lord. So... Do you really want to see if this can kill you or not?"

"Leon, please," Tanya said, "He has a point. Let them go!"

"Our mission is to kill The Doctor and anypony who follows him. Princess Celestia will have us killed!" Agent Leon argued, "I will not let him go!"

"Forgive me Leon," Tanya said, hitting Leon in the back of the head, "Now go, before I change my mind."

"Thank you.. Twilight, carry Applejack and follow me." Doctor Whooves commanded.

Twilight carried Applejack while following Doctor Whooves to The Tardis. Applejack bobbed up and down while Twilight ran, making her feel every ounce of the pain in her leg, she let out a yelp from the pain.

"Twilight, can you please slow down?" Applejack groaned.

"No time. We have to get out of here," Twilight responded.

"It hurts too much."

"See if this works," Doctor Whooves said pulling out his Sonic Screw Driver and pointing it at Applejack while pressing the button.

"What did you do?" Applejack asked.

"I suppressed the pain. The wounds aren't gone, but the pain is minimized."

"Thank... you... Doc..." Applejack voice faded.

"What did you do?" Twilight asked.

"I made her fall asleep, but I need to tell you something."

"What is it?"

"When the goon knocked me out, I had an image. The image was Trixie sending me a message. Telling me that something is coming to Equestria. She said that I'll gain friends, and I'll loose friends and that Friends will become enemies and enemies will become friends and ever action and reaction I make will be the fate of this whole entire planet. Which is odd, because when I went to Appleloosa a dragon picked me up and told me that I was the one who brought them here. I have no idea what this means. But I need to find out. This could explain why Princess Celestia is after me."

"I don't know Doctor. The dragons could be talking about the changelings all those years ago. Not you as in you, but you as in you and all your friends in the war. Your vision could have been just a dream from that encounter. I wouldn't worry about it too much," Twilight assumed.

"But I have had these dreams before. Many times back in the other universe. Well maybe not a lot. But I have had them before."

"Um, Doctor. Agent Leon is right behind us." Twilight warned.

"Then we must run faster."

"I can't, Applejack is weighing me down."

"Just hurry!" Doctor Whooves shouted, "Where are we anyways?"

"We are near Sugar Cube Corner," Twilight responded.

"It looks like we are going the right way then," Doctor Whooves commented.

"Where did you leave The Tardis?" Twilight asked.

"Right beyond this bridge."

Doctor Whooves and Twilight continued to run to The Tardis. Agent Leon picked up speed and was right on their tail Doctor Whooves could see The Tardis coming up into view. Doctor Whooves tried to run faster, but his legs wouldn't let him."

"Twilight, teleport us!" Doctor Whooves shouted.

"Understood," Twilight responded conjuring up a spell. With in a blink of an eye they were inside The Tardis.

"Thank Celestia,"Doctor Whooves said falling to the ground tired.

"Doctor!" Derpy called hugging him.

"Um guys," Twilight turned around, "We have a problem.

"What is it?" Doctor Whooves questioned.

"It's me," Agent Leon grinned.

"How did you get in here?"

"I was in range of Twilight's spell. But now it's time for me to kill you all!

"That wouldn't be a good idea." Doctor Whooves said, playing with the control panel

"Why not?"

Suddenly The Tardis started to shake around. Doctor Whooves and Derpy held on to the structure of The Tardis. Doctor Whooves held on to Dinky, making sure she wouldn't get hurt. Everypony else fell to the ground from the violent shaking. With in a few seconds, the shaking stopped.

"This is way." Doctor Whooves said opening up the door.

"We're in space!" Twilight shouted.

The view was magnificent. They could see space as far as the eye could see along with their planet, with three ships above them.

"Doctor, are those your ships?" Derpy questioned.

"What ships," Doctor Whooves replied.

"Those ships," Derpy pointed, "The three ships above manehatten, ponyville and The Crystal Empire."

"Derpy, go get Dinky, Twilight attend to Applejack."

"What's wrong?" Twilight questioned, "Whose ships are they?"

"Those... those are dalek ships," Doctor Whooves said falling to his knees.

"So, why shouldn't I kill you?" Agent Leon questioned.

"Because, If you kill me, those daleks will destroy your whole planet," Doctor Whooves informed, "It all makes sense now. The dragons were talking about the daleks, my dream was warning me about the daleks. This is probably why Princess Celestia want me dead."

"How many of them in each ship?" Derpy asked.

"Over a thousand, it only takes one dalek to destroy a whole planet without the proper equipment. A thousand daleks was enough to kill the whole human race. Even with weapons like guns and rocket, still wasn't enough to kill the daleks. The only reason why they aren't dead is because I defeated them."

"How do I know that you aren't working with them?" Agent Leon questioned.

"Because you aren't dead. Daleks only have one function and that's to kill. The only emotion they have is hate. No sorrow, happiness, or pity. Just hate and rage. They are simply killing machines."

"I don't know that, you could be lying."

"And I could by lying to Derpy that I love her, or that I am friends with Twilight. They don't know, won't, and can't know that I'm telling the truth. But they trust me. You trusted Princess Celestia when she told you that I'm an enemy. Everything that you have been told in your life may possibly be a lie. But you trust is anyways. Not because you know it's true. But your heart and instincts feel that it's true. If you help me, I can stop the daleks. I can get them to leave this planet."

"How so?" Agent Leon asked.

"I bribe them," Doctor Whooves informed, "Sorry Derpy, but the only way I can do this is if they take me."

"Wait what!" Derpy yelled, "No no no. There must be another way."

"The only other way is by sacrificing ponies lives at least three of them. Maybe more. I can't allow that. I'm sorry," Doctor Whooves said, "I'll try to think of other ways, but if it boils down to it, then I will, and must let them take me. If it means saving this planet."

"What about all your experiments, it'll all get left behind. There will never be answers to them. So many thing left uncovered."

"If it means saving all of you," Doctor Whooves said, "Agent Leon, please let us go. I can save your planet. The daleks are only minutes away from battle, well murder. Everypony you love will die. Do you want that to happen?" Doctor Whooves questioned.

"No, I do not," Agent Leon answered.

"Then let us go. I can stop them without any sacrifices. I can save you, Princess Celestia, and the whole planet."

"I can help by getting rid of you, right here and right now."

"You do that, you'll be stuck in here," Doctor Whooves warned.

"If that's what it takes to save my planet," Agent Leon offered

"You won't be saving the planet, you'll be killing the it!" Doctor Whooves yelled.

"Why can't you just be rational!" Twilight shouted, "I understand you have a mission, but is the mission worth risking the world, or your family?"

"Princess Celestia will banish me to the moon," Agent Leon protested.

"We can worry about that after we take care of the daleks," Doctor Whooves offered.

"Fine, but after this, I'm taking you to the princess." Agent Leon compromised.

"Agreed, but for now, we have a world to save."

Invasion

Leon, can you hear me?" West spoke.

"Loud and clear," Leon responded.

"Long story. Listen, Equestria will be under attack soon. Ponyville, Manehatten and The Crystal Empire are going to be first on the list. I need you to evacuate Ponyville and warn Celestia."

"What's wrong?"

"An alien species is about to attack our planet. Equestria will be first. Just get everypony out of that town."

"Yes sir. West out."

"What's wrong, West?" Tanya asked."

"Equestria apparently is under attack, we need to evacuate Ponyville," West replied.

"By What?"

"Agent Leon never told me."

"Great, we have enemies. And we don't even know who they are this time."

"I'm sure we'll know when we see them. Just get everypony out of Ponyville. I'll go warn The Princess.

"Where do I start?"

"Start with Mayor Mare, She'll warn everypony.

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

"What are we going to do?" Derpy asked frantically.

"Well first we teleport back to Ponyville. Then we warn everypony and get the strong to fight." Doctor Whooves informed.

"So... how do we fight the daleks." Twilight questioned putting her hoof on her chin.

"With these big boys." Doctor Whooves said opening his weapon cache, "The unicorns, who are able to, can use there magic to fight."

"What are those?" Derpy asked, "They look cool."

"I'm not sure," Doctor Whooves wondered himself, "This kid Mickey brought these to my universe from his universe. He never did tell me what they were. One day I'll give them a catchy name. I also started picking up weapons from other planets. Very often I have found my self in the middle of battles, with nothing to defend myself with. So I started to grab other weapons from all sides of the battle. Luckily I have friends who made these guns to kill the daleks and cybermen. I probably would be dead if they came to the rescue."

"Seems like a smart idea to me." Twilight commented.

"I need all of you to take one of these blaster thingies." Doctor Whooves requested.

"They should be called muffin blasters," Derpy smiled, "They look like something I made a while back ago when I was a filly. I made this tube looking thingy and I called them muffin shooters. But muffin blasters sounds better."

"Anyways," Agent Leon jumped in, "Which one of these weapons should we take."

"The big ones. Twilight, I'll need you to find your friends and give them these weapons."

"How many do you have?" Twilight questioned.

"Eh, maybe 300 maybe more,  maybe less."

"How is that even possible?"

"Well The Tardis has unlimited space. I could fit more if I wanted to."

"Ok now lets get to Ponyville, before the daleks get there." Doctor Whooves suggested.

Doctor Whooves went to the panel and set his destination to Ponyville. The Doctor stepped out of The Tardis telling every  everypony to stay inside, while he checked to see if the coast is clear. When he looked up at the sky, he saw a dalek ship hovering over Ponyville. Everypony was running frantically for their lives.

"Everypony run to the blue box!" Doctor Whooves shouted.

"What good will that do?" A random pony questioned.

"Trust me, I'll get you all out of here!"

"You go ahead and die in there. I have a family to look for," She said right before she got killed by a dalek.

"Fleeing will not be tolerated," A dalek said, "You will be exterminated."

"C'mon, get in here. The daleks can't get you inside The Tardis! Doctor Whooves shouted, "Twilight get your friends. I'll keep watch of The Tardis for you. Applejack, Derpy, and Dinky, you'll all stay with me."

"What about me?" Agent Leon asked.

"Take the blaster and follow Twilight," Doctor Whooves ordered, "Take this ear piece as well, It works similar to the way West connected to you."

"How did you know about that device?" Agent Leon questioned.

"I created it. My Tardis will tell me when something of mine is being activated when It's not with me or my companions," Doctor Whooves explained, "I know when somepony's using something of mine."

"Anyways, What are you going to do?"

"I need to make sure that the daleks don't get a hold of this ship. If they do, then they'll be able to destroy all of time and space. Just go, the universe is counting on you two right now."

"Yes Doctor. See you soon."

"Like wise, now get out there and kill some of those daleks." Doctor Whooves said closing The Tardis door.

"Twilight, hold up!" Agent Leon shouted.

"And why should I?" Twilight retorted.

"We need to stick together if we want to live."

"And this is coming from the stallion who wanted me dead a few moments ago."

"It wasn't anything personal."

"You're not as wise as I thought you were. When you are being hunted down to be killed, it's nothing but personal.

"If you want to get mad at anypony, get mad at Princess Celestia, she hired me."

"Just leave me alone. By the way, if you ever try to hurt one of my friends, you'll be begging me to kill you. West is lucky that I didn't do anything when he hurt Applejack."

"Let's just get your friends and get out of this stupid town." Leon said walking aimlessly, "Why did they only send out one dalek?"

"Maybe they are waiting for something," Twilight assumed, "We shouldn't wait though. We need to get my friends and get back to The Tardis as soon as possible. Before the daleks can do anything."

"Maybe the dalek they sent out is just scanning out the area."

"We're going to Sugar Cube Corner first," Twilight insisted.

Twilight and Agent Leon went to Sugar Cube Corner to check on Pinkie Pie. They got to the front door to see that the door has been busted in. Agent Leon gave hoof signals to command Twilight. They walked through quietly trying to see if could her anything unusual.

"Pinkie, are you here?" Twilight whispered.

"Get out of my shop!" a voice shouted.

"Who's that?" Leon asked.

"That's Pinkie Pie," Twilight responded.

The two followed the voice, which led them to a basement. They slowly walked down to see a metal creature. It was able to speak English, but it sounded weird to them. Agent Leon signaled Twilight to stay put, as he crept up on the creature.

"Where is The Doctor?" The dalek interrogated with its monotone voice.

"I don't know!" Pinkie Pie shouted in fear.

"Lies, lies, lies. You know where The Doctor is located."

"I don't know where he is. Last time I saw him, he was with Twilight. I haven't seen him since. I promise."

"You shall be exterminated."

"Over my dead body." Agent Leon said shooting the dalek.

"Oh my gosh. You just saved my life!" Pinkie Pie shouted, giving Agent Leon a hug.

"Is there anypony else here?" Agent Leon questioned.

"No, they are all dead." Pinkie frowned.

"I'm sorry to hear. But we have to go get a few more ponies."

"Where's Twilight? Is she okay?"

"She's upstairs."

"Twilight!" Pinkie Pie shouted, "Are okay?"

"Tell her to wait, or I will kill you." a voice whispered, holding a knife to Twilight's throat.

"Stay down there, Pinkie. Now wouldn't be a good time." Twilight called down.

"Don't be silly, Twilight. We have to get out here." Pinkie Pie called back.

"Who are you?" Twilight whispered.

"You know who I am." The voice replied.

"West," Twilight questioned.

"Yes, and now I have you in my hooves." West responded.

"You sure do," Twilight smiled to herself looking up to see a mirror.

Twilight used a levitation spell to pick up a few knives from the kitchen and quickly pulling them to West's neck

"Either you let me go, or I'll kill you."

"Who are you talking to Pinkie Pie questioned."

"Pinkie Pie, get behind me." Agent Leon whispered, "It may be a dalek, or something."

"If you're going to come up, then at least bring Leon with you!" Twilight shouted down the stairs, "West, let me go, please."

"And why should I?" West questioned.

"I can get you out of here. I can save you, your family and everypony else on this planet. I'm with your partner, Leon. He is down stairs. Give him a call and he'll come up."

"Leon, you down there?" West called.

"Yea, in fact, I'm coming up there right now." Agent Leon responded.

"See," Twilight said dropping the knives, "He's with me right now. Just let me go and I can help you."

"Fine" West said pushing her to the ground.

Twilight got back up and punched West in the face as hard as she could. West got up getting ready to attack. When West launched after Twilight, he was stopped by Agent Leon.

"Why are you trying to attack her?" Leon questioned.

"She punched me in the face!" West shouted.

"Like you didn't deserve it!" Twilight shouted back, "You held me captive, TWICE. You also hurt Applejack, if that wasn't enough!"

"Leave her alone, West," Leon ordered, "She has every right to be pissed. You would be too if you were in her hooves. Now come on, we have a few ponies to save. Twilight, who's do we need to get?"

"Rainbow Dash, Fluttershy, Apple Bloom, Scootaloo, and Sweetie Belle." Twilight responded.

"Let's go get Rainbow Dash next," Leon ordered.

"We can't, if Rainbow Dash is in the clouds, we won't be able to get her." Twilight added

"We have lungs, don't we?" Agent Leon commented.

"Oh yea."

"Now let's go."

"Leon come in," Doctor Whooves ordered.

"I hear here you, what is it?" Leon replied.

"Come to The Tardis. Tanya has found the others."

"Yes sir, Twilight, West, Pinkie Pie, to The Tardis. Tanya has found the ponies we are looking for.

"Thank Celestia," Twilight said in relief, right before the ship started to send out daleks.

"Let's go quick!" Leon commanded.

Twilight, Pinkie, West, and Leon ran to The Tardis as quick as they could. The buildings around them were being shot at and being put in flames. Ponies were running all over the place trying to get to somewhere safe, and the daleks were everywhere. They had to jump over dead bodies and see through the heavy black smoke.

"C'mon, The Tardis is with in sight. Just a little more!" Agent Leon shouted.

They continued to to run to The Tardis, as West tripped about 100 feet away from The Tardis. Agent Leon noticed and went back to help West out.

"Go without me Leon," West ordered.

"I am not going to leave you," Leon insisted, "I can't leave you."

"I broke my ankle. There's no way I'll make it out of here."

"I can carry you."

"Just go!" West shouted, "Save Equestria, save this planet."

Agent Leon started to walk off, before coming up with an idea, "Take this!" Leon shouted throwing his gun towards West, "Don't let those bastards kill you without a fight!"

"Yes sir."

Agent Leon ran the rest of the way to The Tardis. West stayed behind and started to shoot the daleks in the sky. West killed two or three before they noticed him. West started to crawl the a building closest to his location. He shot about five more daleks while crawling 10 feet away from his original position. He kept crawling until he hit a metal object. West looked up to see a dalek, looking at him.

"Resistance will not be tolerated. You will be exterminated," the dalek said.

"Goodbye Leon." West whispered to himself.

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

"Twilight, Pinkie," Fluttershy cheered in her soft voice, "I'm glad you made it out safely."

"Leon." Tanya called out.

"Yes, Tanya?" Leon on sighed.

"Where's West?"

"He stayed behind."

"What do you mean?"

"He tripped and broke his ankle. I tried to help him up, but he told me to continue without him."

"And you listened to him!?"

"We both would have been killed."

"We can't sit here and mourn about his death," Doctor Whooves said, "We must move on"

"Wait," Pinkie pie said, "Where's Octavia and Vinyl Scratch?"

"I don't know, but we can't stay here" Doctor Whooves said.

"Wait!"

"What was that?" Twilight asked.

"It's The Tardis, it's picking up somepony with in the radius of The Tardis. They're calling to us, "Doctor Whooves informed opening The Tardis door.

"Octavia, we must hurry!" Vinyl Scratch yelled.

"Hurry!" Doctor Whooves called out.

Octavia and Vinyl Scratch continued to run to The Tardis, while Octavia got shot by a dalek. The only sound there was of Octavia was the sound of her body hitting the ground.

"OCTAVIA!" Vinyl Scratch shouted.

"Leave her!" Doctor Whooves shouted, "She's dead."

"No, I can't!" Vinyl Scratch shouted back.

"C'mon!" Doctor Whooves argued right before she got killed by a dalek, "Dammit!" Doctor Whooves shouted.

"What happened?" Twilight questioned.

"We're getting out of here." Doctor Whooves said.

"What about Vinyl and Octi?" Pinkie Pie asked.

"They're dead!" Doctor Whooves shouted, "Now hold tight, we are going to the Chrystal Empire."

"Why the Crystal Empire?" Rainbow Dash questioned.

"I need to set some things straight with Celestia," Doctor Whooves responded, "Leon, Tanya, if you do anything to try and hurt me, Derpy, my daughter, I will kill you two without any second thoughts."

"What did they do?" Pinkie Pie questioned.

"They tried to kill me, which I could care less about, but when my wife and daughter gets involved, I'm going to do what any father and husband would do to protect them. I'm sure you wouldn't understand Leon."

"But I would." Agent Leon jumped in to defend himself.

"And how's that?"

"My family was killed during the changeling war, both wife and son. When my family died, I wanted nothing more than to keep Equestria safe. When Princess Celestia told me you were an alien species, I wanted to make sure nopony else would go through what I went through. Although I'm sure many did during the war. But it doesn't matter haha, now our whole planet is going to get destroyed. Why did you do this Celestia?"

"So the only reason why Celestia wanted me dead, was because I'm not a pony. Because I'm a different species. Hope she knows that I have a heart, well two for that matter. I'd be better off if i didn't regenerate all those years ago."

"Don't think like that," Derpy said, "If you had died, we wouldn't be here right now."

"If I had died, then the daleks wouldn't be here. You wouldn't be on Celestia's hit list, Applejack wouldn't have been hurt, Octavia and Vinyl would still be alive. The whole world would be a better place."

"If you are a time traveler, can't you go back in time and fix this?" Applejack asked.

"I can't go back and change fixed points in time. I can't make contact with ponies I know, for example, I can't go back to my wedding day, because if we were to see me it can mess up the timeline and bunch of complicated things that i'd much rather not get into right now."

"What do we do?" Twilight asked.

"We get rid of the daleks, but first lets go inside we need to talk to the Princess."

Captured

"Here we are guy," Doctor Whooves informed poking his head out of The Tardis, "We are in Princess Celestia's palace. Leon, I need you and Tanya to The Princess and tell her that you have me, Twilight, and Derpy captured."

"Yes sir," Agent Leon acknowledged.

"Hurry, before the guards show up."

Agent Leon and Tanya ran up to the entrance to the throne room, "Permission to enter Ma'am," Agent Leon called.

"Permission granted," Princess Celestia said while looking out at the window.

"We have found The Doctor and his wife, plus the traitor," Tanya informed.

"Bring them to me," Princess Celestia ordered.

"Yes, your majesty."

"Doctor, we are headed your way," Agent Leon whispered.

"Good," Doctor Whooves said, "Derpy and Twilight, you two with me. Everypony else, get out of The Tardis before me and walk away from it. Don't make eye contact with at all, act like you don't know what it is."

"Yes, Doctor." They replied in unison.

"Applejack," Doctor Whooves turned around as he walked to the door.

"Yes?" Applejack replied.

"Take care of Dinky for me."

"I will."

Everypony left The Tardis leaving Doctor Whooves, Derpy, and Twilight in The Tardis. Shortly after they left, Agent Leon called out through the headset.

"Doctor, we are right outside The Tardis," Agent Leon informed.

Doctor Whooves, Derpy, and Twilight stepped out of The Tardis and followed Agent Leon to Princess Celestia. A minute later they were in the throne room, "Princess Celestia, we have the prisoners right here," Agent Leon informed opening the doors.

"Good," Princess Celestia smiled, "Give them a chance to speak before taking them away. Twilight, you first. Why did you betray me?"

"I couldn't let you kill them," Twilight responded.

"And why exactly couldn't you?"

"Because of what he has done for us. He has saved Equestria from the war. He made sure that we stayed and fight. He got rid of Discord, Queen Chrysalis, and King Sombra. If it wasn't for him we would all be dead, or enslaved."

"Continue," Princess Celestia ordered.

"He is also working on a way to stop the weird things in The Everfree Forest from happening. Tell her Doctor.

"Yes, please do Doctor," Princess Celestia encouraged.

"I have found aura around the cells of a rat. It looks like it was from a spell. I was going to take samples from plants and other animals, but you sent your little buddies after me, and trashed my house." Doctor Whooves ranted, "Now for more important questions, why are you doing this to us?" Doctor Whooves questioned, "Why are you trying to get rid of me and my family?"

"To keep country safe," Princess Celestia replied.

"To keep this country safe!? Derpy shouted, "He saved you from King Sombra, Discord, and Queen Chrysalis~"

"I can't have an alien species in Equestria," Princess Celestia stated

"It's not because of that!" Derpy argued, "You know The Doctor is more powerful than you. You're afraid that he's going to overthrow you. I mean you couldn't save your own country. But he could, that must show who the real hero is. One thing that you don't know though. He does this for more than just our country. He does out of his own free will. He never once thought about taking over your throne. Nor does he want to."

"Doctor, maybe you should tell her about the daleks," Twilight suggested.

"She already knows about them," Agent Leon said, She knows everything that's happened. She knew far before I told her, that Twilight was going to help you. She knows all of your friends are on your side."

"I'm very disappointed in you Twilight," Princess Celestia frowned.

"Princess, I can help you with the daleks. I can end this, nopony else has to die," Doctor Whooves offered.

"I don't need your help. I'm not in any danger at all. The daleks knew you were here. They asked me to bring you to them. You fell right into their trap."

"You're working with them!" Tanya shouted.

"You are making a huge mistake!" Doctor Whooves shouted.

"How so?" Princess Celestia questioned.

"These daleks want nothing but power. They will take over this planet. They will kill you all," Doctor Whooves warned clinching his teeth.

"They said they'll leave right after they kill you."

"They want me dead so I can't stop their plans!" Doctor Whooves shouted.

"Their plans for what?"

"To take over the universe!" Doctor Whooves yelled, "If they don't kill you, they'll make you into slaves. The second choice isn't likely."

"And why should we believe you?" Agent Leon questioned grabbing a hold of his hooves making sure he get move.

"Because, they destroyed my planet. They killed all of my species. I am the only time lord left. They tried to destroy planet earth. They tried to destroy all of existence from every universe."

"C'mon Celestia, I know you are smarter than this!" Derpy shouted.

"Agent Tanya," Princess Celestia called.

"Yes, your majesty?" Tanya responded.

"Take Derpy and Twilight away, guards, call in the daleks."

"Yes, Ma'am," The guards responded.

"Don't you dare hurt them!" Doctor Whooves yelled.

"And what are going to do about it?" Princess Celestia laughed.

"Doctor!" Derpy shouted while being dragged out of the room.

"Right this way," One of the guards said with a dalek following.

"Victory is now ours," The dalek said, "Your planet will be spared."

"What do you mean?" Princess Celestia questioned.

"Your planet will work for us"

"He's going to enslave your planet!" Doctor Whooves shouted, "I can stop it. I can save your species, I can save the universe, I've done it many times before, I can do it again!"

"Guards, take The Doctor away. I don't want to hear his nonsense," Princess Commanded.

"Princess Celestia, You're making a huge mistake!" Doctor Whooves shouted as the guards dragged him away.

"ENOUGH!!!" Princess Celestia shouted slamming the doors after Doctor Whooves exited the room, "So how are we going to rule this planet?"

"There is no we," The dalek responded, "I am to kill any threat to our race. You are a threat. You must be exterminated."

"No, wait we can work something out!" Princess Celestia shouted as she covered her face.

"Daleks do not negotiate. You will be exterminated."

"You have three seconds to get away from her."

"Tanya, is that you?"

"Princess Celestia, hurry and get out of here, I'll take care of this machine," Tanya ordered.

Princess Celestia used a spell to blind the dalek. She then flew out of the room as quick as she could. After a few seconds the dalek was able to see again. The dalek noticed that Princess Celestia was no longer in the room. The dalek then turned around to face Tanya who was aiming a weapon at the dalek. Tanya tried to shoot the dalek but nothing came out of the weapon.

"Of course it would stop working when I need it the most," Tanya thought to herself.

"Exterminate," The dalek said.

Tanya closed her eyes knowing her time was up, when she felt a pony somepony touching her shoulder, "It's okay, I'm here," Agent Leon assured as he shot the dalek with the cannon from The Doctor.

"Where's Twilight and Derpy?" Tanya asked.

"In a cell. I told them to keep quiet until I got back. I told them why I did what I did. It was the only way to assure that The Doctor could do what he needs to do. The Doctor will still probably be pissed at me, so it's going to take the both of us to convince him that we are on his side."

"Yea, that wont be easy. Thanks for saving me though," Tanya added.

"I'm not going to loose you too," Agent Leon confirmed, "But we have to find The Doctor. The Doctor has the most information about these things. If he can get rid of the daleks, then Equestria will be safe again."

"What about Princess Celestia?" Tanya questioned.

"I can care less about her. She betrayed her country, including you and I. She's the one who got West killed. Whether she knows it or not. I can't trust her anymore. Just follow The Doctor and we'll be fine," Agent Leon assured, "Let's just go find The Doctor. He'll get us out of this mess."

"I hope so," Tanya frowned.

"Doctor come in," Agent Leon said putting his hoof to his ear, "Can you hear me?"

"Look, somepony misses you, "The guard laughed, "How cute."

"C'mon, let me go. You're making a big mistake," Doctor Whooves warned trying to wiggle his hooves out of the shackles that are holding him to a table.

"You sound just like my mother... I hate my mother."

"Those daleks will destroy your planet. Even after my death they'll take you as slaves. They'll use you to fight for them, or they'll kill you all."

"Sure they will," The guard laughed, "And I'm going to the first pony who will walk the moon. Let me tell ya, you crack me up real well. It's a shame that I have to kill you."

"Why wont you listen to!" Doctor Whooves shouted, "I want to save you. I want to save your planet!"

"No, you want it for yourself." The guard assumed.

"If that was true, you would have known years ago. Just let me go!"

"I'm sorry, but these are orders from The Princess."

"Your Princess has killed several innocent ponies, including Octavia and Vinyl Scratch. She has betrayed you!"

"I'm sorry," The guard said picking up a syringe, "This wont hurt a bit."

"Put that down right now," Applejack said in a soft but stern voice.

"Applejack?" Doctor Whooves questioned.

"And how are you going to do that?" The guard taunted, picking up a scalpel

"By force," Applejack grinned as Rainbow Dash and Pinkie Pie walked in.

"You might not want to tick me off. I haven't had the best day," Rainbow Dash warned, "I'm going to give you one chance to put those sharp objects down and walk off, before somepony gets hurt."

"Nopony messes with my friends. NOPONY!" Pinkie Pie shouted.

"Okay okay, I'll let him go. Just please don't hurt me," The guard pleaded as he dropped the scalpel and syringe."

"That's what I thought," Applejack laughed, "Not as tough as you look. Now leave."

Pinkie Pie and Applejack untied The Doctorfrom the table, while Rainbow Dash stood guard at the door, "Thank you so much," Doctor Whooves said gracefully, hugging Applejack and Pinkie Pie, "How'd you know I was in trouble?"

"Saw the guard drag you this way," Applejack replied.

"Simple enough," Doctor Whooves shrugged, "We have to stop meeting up like this."

"Indeed."

"Doctor, are you there?" Agent Leon asked.

Doctor Whooves Picked up the head forcefully, "What do you want!"

"I'm coming for you."

"Why, so you can kill me yourself?"

"No, I want to make amends," Agent Leon said softly.

"You can forget about it. I'm going to go to the throne room and you are going take me to my wife. I'm going to get rid of the daleks and you're going to leave me and my friends alone. Do you understand!" Doctor Whooves yelled.

"Yes, Doctor," Agent Leon responded, hanging up the line.

"Where's Dinky?" Doctor Whooves asked.

"She's with Fluttershy." Applejack informed, "Don't worry they are in a room with Sweetie Belle, my sister, my cousin, and Scootaloo."

"Good, now follow me," Doctor Whooves commanded.

"Um, Doctor." Rainbow Dash whispered, "There are three daleks coming. They are all the way at the end of the hall.

"Everypony, hide," Doctor Whooves whispered.

"No need." Applejack said, "Not with these weapons."

"Good point," Doctor Whooves responded, "New plan. Hide behind those doors and wait for them to come through. When they come through, we open fire."

"Got it." Rainbow Dash confirmed.

They waited a few moments, but the daleks wouldn't come through the door way. Doctor Whooves grew inpatient by standing there and waiting, "Applejack, peek your head through the door way and see if they're still commanded.

"Yes, Doctor," Applejack replied as she poked her head out. She saw Tanya and Leon walking towards their location, with three dead daleks, "It's Tanya and Leon," Applejack informed.

"You guys can come out now!" Tanya called.

"The path behind us is clear," Agent Leon informed.

"Take me to my wife now!" Doctor Whooves shouted.

"I will, just calm down."

"How can I calm down. This whole world is under attack all because of me. All of you guys are going to die."

"Not if we work together," Applejack said.

"Doctor, you are the only one who can save our planet," Agent Leon said, "If you give up, then yes we will parish. We will help you. Tell us what we need to do to help. '

"I need to know what the dalek's are planning. Only then will I be able to stop them.

"And how will you find that out?" Tanya questioned.

"I board one of their ships," Doctor Whooves informed.

"Not to be rude Sugar Cube, but that's insane. More insane than some of the things that Pinkie Pie does," Applejack stated.

"Yea, I tried to fly off a roof one year during nightmare night."

"Anyways, Leon take me to Derpy and Twilight, "Doctor Whooves requested, "I think I have a plan that'll work,"

"What is it?" Agent Leon asked.

"Oh, you'll find out."

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"Come on. Let us out!" Derpy shouted, "The Doctor needs us."

"Sorry, can't allow it," the guard said.

"Please," Twilight begged, "these daleks will kill as all."

"Can't you just teleport us out of here?" Derpy asked.

"The cells are magic proof. I'd just tire myself," Twilight informed.

"Will you listen to me!" Derpy shouted once more, "We aren't the enemy. Princess Celestia has blinded you!"

"If I let you go, Princess Celestia will kill me," The guard stated.

"Oh come on, is that everypony's excuse now!" Twilight shouted, "My brother would be ashamed of you. Capturing his sister.

"I'm just following orders," The guard replied.

"You're holding one of the Elements captive!" Derpy argued.

"Yes I am and that is your problem."

"And it'll soon be yours," Doctor Whooves threatened, "Let them go."

"Or what?" the guard taunted.

"Or, I can end your life." Doctor Whooves responded after he tackled the guard, "Give me the keys."

"Your kidding right?" the guard laughed.

"Just used the screw driver," Derpy suggested.

"Can't it's a deadbolt."

"What can you possibly do if I don't let them go?" the guard questioned.

"You don't want to know," Doctor Whooves warned.

"Ooh... Look what I have," Pinkie Pie giggled, jiggling the guard's keys, "You should really pay more attention to your surroundings."

"Now get up and leave," Doctor Whooves ordered getting up off the guard, "Pinkie, unlock the cell."

"Okie dokie lokie," Pinkie Pie shouted gleefully as she opened the cell.

"I better not see you again," Agent Leon spoke, as the guard stomped out of the room.

"Okay guys," Doctor Whooves announced, "We need to get going. Applejack lead us to Fluttershy and the fillies."

"Yes sir," Applejack replied.

The whole group followed Applejack to a room that happened to be half way to the opposite end of the palace, "We are here," Applejack informed.

"Okay good. Now that we are all together, I can tell you all my plan. Twilight, I need you to contact the changelings.

"Are you crazy!?" Twilight shouted, "They are our enemy."

"Look, we don't have many options right now. We are highly outnumbered. There are countless amount of changelings, they can distract the daleks buying me time to board one of the ships. With the changelings on our side, there'll be less daleks for me to worry about. Also, if the changelings can transform into a dalek, then we will use that to our advantage."

"Doctor, the changelings aren't to be trusted," Applejack argued.

"Any why is that?" Doctor Whooves asked.

"They are deceitful."

"And that's exactly what we need. The daleks are smart, but they can't repel something they don't know about."

"I guess you're right."

"One problem," Twilight informed, "I have no way to contact the changelings."

"Im pretty sure The Princess of the Night wont mind helping us out," Doctor Whooves assured, "Where is Luna."

"She's in Canterlot. We share the same castle." Twilight responded.

"Okay, to The Tardis as fast as you can. Doctor Whooves ordered, "The daleks probably know that we are here and are probably on their way. Why they haven't found us yet? I don't know, but they should be closing in on our position."

Everypony ran to The Tardis. The guard from the dungeon was following them, with their knowledge. The guard was aiming his horn trying to get a steady shot on The Doctor. Tanya and Leon stayed behind the group, making sure that nopony got left behind. The guard shot a beam at the herd before they could turn the corner to The Tardis. Tanya was the last pony to turn the corner and the one who got hit with the beam. Tanya fell to the ground and gave a yelp of pain.

"Tanya!" Agent Leon shouted.

"Leave me, I'll hold them off," Tanya informed.

"Where'd you get shot?"

"My leg, don't worry about me though," Tanya said trying to get up, "Get out of here, before they come. Don't worry I'll catch up."

"The Doctor may not wait."

"I'm ok with that. Just make sure he finishes the job."

"I will," Agent Leon said as he ran off to The Tardis.

"I will not let you pass!" Tanya shouted.

"Then you'll die with them," the guard replied.

"It'd be my pleasure."

The guard ran up to Tanya and tried to tackle her. Even with her wounded leg, she was able to dodge him, "C'mon, you can do better than that." Tanya taunted.

The guard pulled out a knife and tried to stab Tanya. Tanya grabbed his hoof as he ran towards her, and pushed him away. The guard turned around and tried to stab her again, but Tanya tripped him, making him fall to the ground. She dropped herself, with her elbow pointed at his stomach. The guard rolled over causing Tanya's elbow to hit the cobblestone floor.

"Don't underestimate me!" the guard shouted.

"Trust me, I haven't, "Tanya replied.

Tanya crawled to a nearby staircase, taking notice of the railing. The guard followed Tanya to the stair case and picked her up by the throat, giving a loose enough grip to let Tanya speak, "Any last words?" the guard questioned, knowing that he won.

"This is where you loose," Tanya grinned. Tanya pulled our her hoofcuffs, ringing one cuff on the guards hoof, and the other cuff on the railing. The guard threw Tanya down the stairs as he yelled at her. Tanya broke her arm, but still crawled away from the guard's position. She heard a dalek approach from the staircase.

"Hey there, Dalek, can you get me out of here?" the guard asked.

"Daleks do not help enemies. Daleks do not accept requests." The Dalek responded.

"Please?" the guard begged.

"You will be exterminated."

"No, please. I have a wife and two foals. I need to take care of them."

"You failed them," The dalek said as he shot the guard.

"Looks like the dalek is going to kill me, or I'm going to bleed to death from the beam," Tanya whispered to herself, "Hmm." Tanya said pulling out a headset that the doctor gave her, "Of course it's broken, well only a few minutes till I die,"

The dalek heard a few whispers coming down the stairs and found Tanya breathing heavily, "Please make it quick. Let the pain go away."

"You aren't destined to die yet," the dalek said.

"Kill me!" Tanya shouted.

"It's not time. Universe is not ready for your death."

"What are you doing here? Why did come to Equestria? Why can't you leave us alone?"

"We are here for The Doctor."

"One of you guys said that, you were going t enslave us."

"That's none of your concern."

"How the hell is this none of my concern. My friends will be stuck in chains! Of course I'm concerned. Now tell me your plans!"

"The daleks are going to take over the universe, all the universes. Every living will bow down to us."

"You are crazy!" Tanya shouted.

"No, we are brilliant."

"In what universe!?"

"All of them."

"How are you going to take over the universe?"

"The Tardis," the dalek informed.

"If you think The Doctor will give up The Tardis, then you are strongly mistaking."

"The Doctor will give up The Tardis, even if it's by force."

"He will stop you."

dreams

"Wake up."

"Huh, where am I? Who said that?" Doctor Whooves

"It's okay." The voice grew closer.

"Why do I only see black?"

"You are safe here."

"Show yourself!" Doctor Whooves demanded.

"I already have." The voice appeared in front of Doctor Whooves.

"Trixie, I thought you were dead."

"I am. And this isn't Trixie. This is your subconscious mind. It has taken a form of somepony that you trust completely and that you're most comfortable with so this message can be sent peacefully."

"Why you though? Why not Derpy, Dinky, or any of the companions I have had before I came to this universe?"

"I don't know, but that doesn't matter now. What matters is this message." Trixie said.

"What message."

"There is a foe headed this way. This will be the biggest challenge you will ever face."

"What foe? What are you talking about?"

"Your biggest fear is coming, and it has been for years now. Many will be in danger. Even after your death will they parish."

"Why are you telling me this?" Doctor Whooves questioned.

"I don't know. I am you." Trixie said.

"Yea that sounds weird coming from you. Maybe it was one of my past reincarnations, or my human self, or maybe even Donna Noble. But coming from you, that's creepy."

"Doctor, focus. What is about to happen will be your biggest challenge. You will loose friends. You will gain friends. Enemies will become friends. Friends will become enemies. Your actions and reactions will be the fate of Equestria."

"What am I supposed to do? What is coming?"

"I only know as much as you do. This is all old news to you. You've secretly known this for a while now."

"This makes no sense."

"Whether it makes sense or not. You need to prepare yourself. Mentally and emotionally."

"So on other hands, you don't know what's coming. You only know that it is" Doctor whooves assumed

"I don't even know if something is coming. This is all a dream. We both know that dreams aren't real." Trixie stated

"This is no help to me at all." Doctor Whooves complained.

"Maybe next time, you should check your back. Just in case somepony sneaks up on you." The voice said, turning into a reflection of himself.

"So is this you mocking me?"

"You've been asleep long enough," His reflection stated.

"No I need answers."

"Like I said. This is your subconsciousness. I know as much as you do. I feel what you feel and I hear what you hear."

"Just tell me...Who's coming!?

"When time comes, then you will know." His reflection said fading away.

"I've said you've been asleep for long enough!" Another voice shouted, right before a powerful force hit Doctor Whooves.