Doctor Whooves and The Lone Dalek

by Whooves235

Rating: teen
Tags: Adventure, Derpy Hooves, Violence, Slice of Life, Crossover, Alternate Universe, Doctor Whooves, Main 6, Doctor Who, Original Character, My Little Pony: Friendship is Magic, Mystery
Length: 12797

When Ponies start to disappear all across Equestria The Main 6 are asked by Celestia to go to and investigate, however soon they to disappear. So now its up to The Doctor and Zap Apple to find them before Equestria loses its only protectors

Ponies are disappearing all across Equestria, and it seems that there is strange magic at work so start Celestia sends The Main 6 to go to and investigate, however after a day it seems that they to have disappeared. So now it's up to The Doctor, Derpy, and Zap Apple to find them before Equestria loses its only protectors!!

Published 2019-12-16 19:50:02 UTC
Last updated 2021-05-30 22:23:10 UTC

Chapter 1: The Disappearances

Chapter 1: Golden Son

Equestrian History Museum - Canterlot

As Celestia walked into the building, she took a look around. So many parts of history lay inside these walls, from the founding of the three tribes, all the way to Discord’s defeat. However today she was not here to explore Equestrian history.

“Your Majesty, the crime scene is right this way,” the guard pony said.

“What is the issue?” Celestia said.

“The museum manager, Yellow Thunder; he was found dead,” the guard pony said. “Somepony hid the body, it seems like he has been dead for some time.”

“How long has it been since he died?” Celestia asked.

“The janitor smelled something foul from the Neighipt exhibit. It seems whoever killed Yellow Thunder stuffed the body in a Neighipt Casket,” the guard pony said. “Judging by the fact that the body could be smelled through a casket, I would say that he was murdered some time ago.”

“Take me to the body, I wish to examine it.”

“Yes, Your Majesty.” As the two walked into the Neighipt Exhibit, Celestia immediately caught the scent of the body. She continued walking until she reached the rest of the guards.

“You may leave us,” Celestia said. As the rest of the guards walked away, she examined the surrounding areas. It seemed that nothing was damaged or stolen. “Remove the blanket.”

As the guard removed the blanket, Celestia saw the body before her: it was covered in clumps of flesh and the skin was green. “Like we said before, he had been missing for months, so he has been dead for some time.”

“Do we know the cause of death?” Celestia asked.

“That is why we called you, Celestia. Under normal circumstances, we would call the proper authorities but his on-scene autopsy shows no signs of death,” the guard explained. “No gashes, holes, signs of struggle, and no signs of a blunt object mark. It is as if he just dropped dead instantly.”

“Did you check for magic residue?” Celestia asked.

“Yes ma’am, but there were no signs of unicorn magic present.”

“This is indeed a mysterious event. I will contact Princess Twilight as soon as I can, perhaps she can help with the answer,” Celestia said.

“I understand, ma’am,” the guard said, then walked off to join the rest of the guards. As Celestia walked to the office she noticed the office space. It was messy and quite disorganized; she was used to the cleanliness of her office and the Canterlot Library, but she did expect this type of atmosphere from ponies. As she approached the desk she viewed the files that were presented; many of them looked to be old, but one of the folders stood out, marked File: Golden Son.

“How did this get here?” Celestia asked. She grabbed the folder and then, using her magic, teleported it to an undisclosed location. She continued looking around the office, finding nothing of importance.

“Your Majesty?” a guard said. Celestia jumped in surprise and turned around to face the guard.

“Yes, what is it?” Celestia asked.

“We are waiting for your command ma’am, what should we do?”

“I want you to continue looking around the Museum. If you find anything please alert me at once,” Celestia said.

“Yes ma’am.”

“Now if you would excuse me I must go, I have pressing matters to attend to,” Celestia said. She walked past the guard and to the door of the museum, then took off and flew to the castle.

Canterlot Castle

As Celestia landed on her balcony she entered her room. Walking past her bed she approached her desk. She saw that the Golden Son file had been successfully moved here, and by the looks of it nopony had seen it yet. As she opened the folder she read through it, making sure it was the real thing. As soon as she confirmed her suspicions she closed the folder.

“I must not let anypony find out about this,” Celestia said in a worried tone. “If this information were to get out, it would mean devastation.”

As Celestia paced back and forth she thought about what she could do. If this folder was able to be found by a regular pony, then it could have easily been found by somepony like Twilight or worse, Luna. “I need to find a distraction, something to take the pressure off of this killing,” Celestia said, then levitated some Equestrian Incident Files over to her, quietly reading them out loud.

“Timberwolf Protests in Manehattan, Fires in east Canterlot,” Celestia said. “Hmm, what’s this?¨ As she looked at the folder Celestia cracked a smile. “This should take the attention off of the museum incident.”

Celestia levitated a piece of paper to her desk. She connected the folder she had found, and then began to write.

Dear Twilight Sparkle.....

Ponyville

Twilight Sparkle was many things: The Element of Magic, The Princess Of Equestria, The Future Headmare of The School Of Friendship. But all she wanted to be right now was to be a normal pony, with normal duties.

“All right Twilight, it says right here that next on our list is to go to the grand reopening of Strawberry Sunrise’s Strawberry Shop," Spike said, reading off the list, “then after that we need to go to the post office and pick up some daily letters for Mayor Mare.”

“Spike, how much longer are we going to be at this?” Twilight sighed.

“Twilight, what's wrong? Usually you're all for getting lists done,” Spike asked.

“I’m sorry Spike, but I've just been so tired lately, with Flurry Heart living with us it seems like I have no free time on my hands,” Twilight said, looking down. “I just wish I had something to do that I could enjoy.”

“Twilight, you know as well as I do that Ponyville needs you. Ever since Tirek’s attack, the town has been flipped upside down, shops destroyed, families separated,” Spike explained, “And it's your job as a Princess to make sure that all of these things are seen to.”

“I know, Spike, but lately all of our friends are busy,” Twilight said. “Pinkie is busy with Flurry, Fluttershy and Discord are busy planning their marriage, and Applejack and Rainbow have to take care of Zap,” Twilight said. “And then you and Ember are seeing each other all the time.”

Spike blushed at the thought of Ember. “Well I mean, it's not like I can't say no, Twilight. She’s really given me a sense of happiness in my life,” Spike said. “And besides, Rarity is still free to hang out with.”

“Rarity is still busy with her fashion business, and with her injuries she has been inside more often,”Twilight said. “It seems like everyone has moved on with their lives, and meanwhile I'm stuck here wishing that things are the way they used to be.”

“Things change, Twilight. We may not like them, but we have to accept them,” Spike said. “Besides, if things were back to the way they used to be, then you and Pinkie would have never become filly friends.”

Twilight smiled at the thought of Pinkie, how even when she was in the worst moods, Pinkie was there for her.

“Yeah, I guess you’re right, Spike.”

“There's that smile,” Spike said. “Now let's go, this list won’t complete itself!”

As Twilight and Spike walked down the neighborhood, a blue light shined in the corner, and it slowly followed the two until they were out of sight.

Sweet Apple-Dash Acres

"Applejack!” Rainbow shouted. “Where is that package that was left on the table!”

Applejack popped out of the corner of the room. She had flower all over her muzzle. “How should I know? I'm not the one who ordered 12 Daring Do books!”

“They are limited edition, Applejack! L I M I T E D!!” Rainbow said, tossing her hooves in the air.

“Well I wonder who else could have possibly grabbed them,” Applejack stared blankly at her wife. “Maybe it’s the other Daring Do fan in the house.”

“Ohhhh.” Rainbow facehoofed. “Right… Zap.”

“Where is that darn colt?” Applejack asked. “He has chores to do today.”

“I think he is with the CMC,” Rainbow said. “Scootaloo probably wanted his help with some crusading stuff.”

“Scootaloo is a grown mare, I would think she can take care of herself,” Applejack said. “Then again, she is your daughter.”

“What's that supposed to mean?” Rainbow said.

“You’re so cute when you’re angry.” Applejack chuckled. “I'm just playing with you, Dashie.”

“Whatever.” Rainbow crossed her hooves, a tiny blush coming to her face.

“Well I need Zap to come back home, so you grab him and tell our daughter that she can grab him after he is done with his chores¨

“All right, Applejack,” Rainbow said. “I’ll be right back.” She then opened the barn door and took off to the CMC clubhouse.

The TARDIS

“Where is that bloody machine?” Doctor Whooves said. He walked around the console room, opening and closing different wall storage rooms. “Derpy! have you seen my machine?”

A grey pegasus wandered into the room, with bubbles as a cutie mark. Her most distinctive feature, however, were her eyes. “What machine, Doctor? You have a lot…”

“It’s the machine that goes ding,” The Doctor said. “Or is it the one that goes beep? I can never remember.” He put his hoof to his chin, thinking about the machine.

“Is it this one, Doctor?” Derpy held out a strange-looking box with glowing buttons and wires showing.

“No, that's the machine that goes blorp,” The Doctor said. “Luckily I haven’t had to use that since…”

And as if by magic, the machine started to make a sound, which caused Derpy to drop it in fear. “Doctor, I think your machine is broken.”

“It’s all right Mrs. Doo, that just means that there’s a time anomaly detected,” The Doctor said. “Looks like adventure calls!”

“Oh boy, another adventure!” Derpy said, smiling. “Where are we going this time, Doctor?”

“Wherever fate takes us!!” The Doctor ran to the TARDIS control panel and flipped a lever “Allons-y!”

Carousel Boutique

Rarity was a pony of many talents. She was a dressmaker, fashionista, and a beauty stylist. But above all the one thing she was known for was her generosity, her compassion for others is what made her one of the Elements of Harmony. However, lately she was more or less contemplating on what she does for a life.

"Rarity? Are you here?" Sweetie Belle said from her room. She walked down the stairs to find Rarity sitting in the kitchen, and next to her was a cup of coffee and a necklace she had been working on.

"I'm right here, Sweetie Belle," Rarity said. "Is something wrong?"

"I just wanted to tell you that I'm going out, and I won't be back till this evening.”

"And where pray tell might you be going?" Rarity asked, her curiosity piqued.

"Button Mash is taking me out for a movie, and then we are going to dinner," Sweetie said.

"Oh, you and that Button make such a cute couple!" Rarity said, then saw her sister get a tint of red to her cheeks. "He is so lucky to have you as his marefriend."

"Thanks, Rarity," Sweetie said. As she headed to the door Rarity took a sip of her coffee.

"Sweetie, may I ask you something?"

"Yeah, Rarity?"

"When you first felt feelings for Button, what was it like?"

"Gosh, I...I don't really know how to describe it," Sweetie said. "It’s kinda like your mind does what you feel is right, your body starts to shake, but...in a good way. Also you have this urge to be with them, no matter where they are."

"You really do love him, don't you?"

"I would do anything for Button," Sweetie said in a stern voice. She walked over to her sister, and could see something was bothering her. "What's wrong, Rarity? You haven’t been yourself lately, ever since Tirek you’ve been more quiet than usual"

"Sweetie, it's hard to describe," Rarity said. "After everything that’s happened to us, it seems like all of my friends have somepony to go back to. Twilight has Pinkie, Fluttershy has Discord, and Applejack and Rainbow have each other." Rarity then paused and looked out the window "And now there is just me...I don't have anypony, nor would anypony want to date somepony like me

"Rarity, don’t talk like that!" Sweetie shouted. "You’re the best pony I know and any stallion or mare would be lucky to have you!"

"Who would want an old, scared, broken-horned, missing-eyed unicorn like me?" Rarity said, touching what was left of her horn.

"There’s somepony out there for you Rarity, you just have to look," Sweetie said, then leaned over and kissed her sister on the forehead. She walked to the door. "Just wait, Rarity, someday you’ll meet that special somepony." She then closed the door, leaving Rarity to herself, and the words that were last spoken.

"Who is the right pony for me..."

Chapter 2: Gone

Chapter 2: The Disappearances

Twilight's Castle/Map Room

"Well that took longer than expected," Twilight said, walking into the Map Room. She sat down on her throne and put her head back in exhaustion. "Who would have thought that a post office would take that long to open?"

"Well, they were missing a few people," Spike said. He flew over to a bowl of gems and began to have a snack. "Besides, now we have the rest of the day to spend with Pinkie and Flurry."

"Not exactly," Twilight said. "Pinkie took Flurry to Sugarcube Corner to help with the Cake Twins. Now that they’re running the shop they need some help knowing what exactly to do."

"Oh right..." Spike said as he tossed a gem inside his mouth, then began to choke a little.

"Spike, what's wrong?" Twilight asked, holding up.

He then coughed up the gem he ate and he began to burp until he breathed his Dragon Fire, and a note emerged from the fire. "I think we got a letter," Spike said, then collapsed on the floor.

"Oh! Its a letter from Celestia." Twilight said. "She must need some help in Canterlot, knowing her." She then opened the letter and read the following note, her eyes going wide a bit. "Spike listen to this!"

Dear Twilight,

I would not be writing to you under normal circumstances unless it was important. Enclosed in the following document is an Equestrian Police report. According to the report, ponies have been disappearing across Equestria. From Appaloosa to Ponyville there have been ponies disappearing. Normally I would have the Royal Guard do this job, but things have come up in Canterlot that require my presence. I am sure that you and your friends will have this mystery solved quickly. Included with the previously mentioned document is a map with the locations of disappearances. The fate of Equestria’s citizens lies with you.

Warmest regards,Princess Celestia

"Ponies disappearing?" Spike said. "You would think we would have noticed that."

"Well that would explain why the post office had to deal with such a long wait for the grand opening," Twilight said. She opened the envelope and looked at the map. "Spike, we need to get the girls. This situation is serious."

"Alright, I’m going to go get Fluttershy and Rarity. You can find Rainbow, Applejack, and Pinkie," Spike said. "See you when I get back." He then ran out of the door to get the others with Twilight following behind.

Sweet Apple-Dash Acres

As Rainbow entered, she tried to hide her blush. The same went for Zap, who was trying not to laugh. They saw that Applejack was cleaning up the mess; Applejack looked at Rainbow.

"What did you do?"

"I didn’t do anything! I just walked in!"

"Bullshit. You’ve got that look in your eyes. You did something."

"No I didn’t!" Dash was quiet for a moment. "Look, it wasn’t even that big of a deal-"

"What. Did. You...Do?!" Applejack demanded sternly.

"I may or may not have accidentally ran into the chicken coup and spooked out all the chickens," Dash said, the blush on her face growing redder.

"Did you clean it up?" Applejack asked.

"Yes, why do you think we took so long!" Rainbow said.

"Good." Applejack smiled, then got up to her face. "And If you ever do anything like that again I will personally see to it that you won’t make it to your next birthday."

"Is it too late to say I love you?" Rainbow asked with a nervous grin.

Applejack just smiled and kissed her wife on the cheek. "Nope," she said, "but I’m serious about that birthday thing."

"Yeah whatever, Apples," Rainbow said. She looked to Zap, who was curiously wondering what exactly he just witnessed. "Zap, how about you go out back and do some of the chores? I'm sure your mother will need more apples by the time she’s done with the fifth pie."

"Uhh...alright mom," Zap said. "Oh, I forgot to tell you: Scootaloo says hi. She wanted to come home but she and Rumble are busy looking for apartments in Manehattan."

"Oh...ok," Rainbow said, slight disappointment in her tone. "I’ll be in the study if you need me, ok?"

"Alright mom," Zap said, then left the house and went to the back. As Rainbow watched him leave she slowly walked to the study. She opened the door and saw the room; it was a simple room with yellow wallpaper and a green flooring to it. The floor was made from a nice tree bark that Applejack’s parents had made before they passed. She sat down on the chair and looked at the wall, the wall of many photos. Applejack called this room The Family Room, because it was in this room where all the family photos went, from Bright Mac and Pear Butters’ wedding all the way to Zap’s birth. However, she was more focused on one photo, in particular, a photo of Rainbow standing next to Scootaloo, who was carrying her highschool diploma, and with it a full college scholarship in Manehattan.

"Rainbow, you in here?" Applejack asked. She found Rainbow in the study, looking at the wall. "Sugercube, you ok?

"She grew up too fast," Rainbow whispered softly.

"Dash, it's going to be ok," Applejack said. "I know ya miss her, but she’s a grown mare now. She has a life, a coltfriend."

"I almost never see her anymore, Jackie," Rainbow said. "It's like I lost a part of me."

"You still have me and Zap," Applejack said.

"Yeah but for how long?" Rainbow said. "Zap is ten and it only seems like yesterday he was born."

"Dash, if we think about the future then we can’t focus on the now," Applejack said. "If we savor the moments we have with our son, then everything will be ok."

"Ma!" Zap said. "Aunt Twilight is here!" The two of them turned around to see Twilight standing at the door to the study, looking quite concerned.

"Twilight, what's wrong? You look like ya seen a ghost," Applejack said.

"I’m sorry to barge in unannounced, but I need you two. It's an emergency," Twilight said.

"¨Why, what's wrong?" Rainbow asked.

"I’ll explain everything later. Right now we need to get to the castle," Twilight said. Zap walked next to Twilight, curious as to what was going on.

"Hey, is everything ok?"

"We can't just leave Zap here," Applejack said.

"I think he’s old enough to take care of himself," Rainbow said. "After all, he is our son."

"Ugh, fine" Applejack said reluctantly. "¨Zap, we’ll be back faster than a jackrabbit on stilts."

"Uhh ok?" Zap said. "What do I do in the meantime?"

"There’s a list of chores on the table in the kitchen," Applejack said as she was pushed out the door by Rainbow.

"OkbyeZapweloveyou!" Rainbow said before closing the door.

"Ok...that...happened," Zap said. He walked over to the list of chores and read them, taking note of what was already done and what needed to be done.

"Alright the faster I do this, the faster I can get back to Daring Doo" Zap smirked

Five Hours Later

As Zap sat in the living room, he continued to read his new Daring Doo book. He had finished his chores over two hours ago, and it had been over five hours since Rainbow and Applejack left on their mission, and Zap was getting worried.

"They’ve never taken this long before," Zap said to himself. He got off his chair and walked over to the front yard, expecting to see his parents returning, arguing as usual only to make up five minutes later. "Maybe they’re just doing some late bucking."

Just then he started to hear a strange sound; it almost sounded like somepony dragging keys along the strings of a broken piano. He turned to the front yard again only to see something he had never seen before: a blue box with the words Police Public Call Box labeled on the top of it. Two ponies stepped out of it.

"According to the machine the disturbance is coming from this time and location," The Doctor said, then walked up to the house porch.

"Doctor, are you sure that there are ponies home?" Derpy said. "It looks like this place is empty."

"Fear not my faithful companion, I have a solution to your problem." He simply knocked on the door. "Hello? This is your apple inspector, I'm here to inspect your apples...and...your...applesauce."

As the door opened Zap stood before the two ponies, he was confused and after what he just heard "Uhh, hi?"

"Hello young colt!" The Doctor said. "Are your parents home? I am the apple inspector and I'm here to..."

"nspect the apples and applesauce?" Zap said. "Yeah I may be a kid, but I definitely know apple inspectors when I see them. Who are you really?"

"Doctor, he’s on to us!" Derpy said.

"Well if you must know, I am The Doctor and this is my companion Derpy. We are here because my machine has picked up a time and space anomaly, and it appears that it is located in this barn."

"Ok, now I'm willing to believe your Apple Inspector story..." Zap said bluntly. "I'm sorry Mr. Doctor, but my mom told me never to let strangers into the barn."

"Well you're in luck, Zap Apple, because I happen to be a friend of your mother's."

"Really?" Zap asked doubtfully.

"Yes, do you want me to prove it?"

"If you’re really a friend of my mom’s, then tell me something only I would know."

"Your mother Rainbow Dash has an addiction to orange juice and your mother Applejack hates it."

"Yeah...that's mom..." Zap said. He stepped aside and let the two ponies enter the house. The Doctor started to wander around the barn a bit, holding a silver box with glowing lights.

"Does he usually do this?" Zap asked Derpy.

"It might look weird at first, but you get used to it."

"I can't imagine," Zap said.

"Derpy, I think I found something!!"

Derpy and Zap followed The Doctor’s voice into the study, where he was standing in front of the photo of Bright Mac and Pair Butter. "Look right here!"

"It's....just a photo" Zap said "What exactly is so important about it?"

"It’s not the photo itself, but rather what it contains," The Doctor said. He carefully took the photo and started to shake it, and a piece of paper fell out of the photo. "Ah ha!!"

"Doctor, what is it?" Derpy asked. The Doctor took out his Sonic Screwdriver and started to scan it.

"Just as I thought, a time anomaly."

"A what?" Zap said.

"A time anomaly, it's sorta like a fragment of time that was misplaced. Other words for it are aberrations, time misplacements," The Doctor said. "The point is this piece of paper did not exist before, but now it does, suggesting something in the past has changed, or rather is changing as we speak."

"Well Doctor, what does the note say?" Derpy asked.

Dear Doctor,

I hope this note finds you. According to Applejack this is the only photo frame that is old enough to be around in this time. From the sentence I have just written you can surmise that me and my friends have somehow been transported into the past; however, we happened to run into a version of yourself who for some reason knows us, suggesting that he is also from the future. He, or rather you, told us that we could not return to the present due to the fact that events will be happening that will be making history. He did, however, tell me to leave this note to make sure that everything goes into its proper place, whatever that means. The point is we are stuck in the past and we can't get back, not yet at least. Please tell Flurry Heart and Pinkie that we are safe and we miss them. Applejack and Rainbow also asked me to tell you to tell Zap that they are ok as well.

From Twilight

"Wait, my moms are trapped in the past?!" Zap shouted.

"Yes, according to Twilight at least. However, what is curious is how exactly they got there," The Doctor said. "If a future version of me is keeping them there it means something big is going to happen."

"Doctor, how far are they trapped in the past?" Derpy asked.

"According to the sonic, Twilight and her friends are trapped in the past over 30 years ago."

"Well if they’re with a past version of you at least they’re safe," Derpy said.

"Doctor, what’s going on?!" Zap shouted. "First you barge into my house. then you say my mothers, as well as my aunts, are trapped 30 years in the past?!”

"Zap, listen to me," The Doctor said, "we are going to find your parents, and find out how this happened."

"But how can you be so sure?" Zap said.

"Because I am The Doctor, and I save People...or...Ponies, rather," he said. "Now then, Zap, where were your parents before they disappeared?"

"Aunt Twilight said something was going on at the castle of friendship."

"Then that's where we will start!!"

Chapter 3: The Stone Pegasus

Ponyville

¨Alright this way¨ Zap said, as he walked down the pathway to the castle ¨My cousin Flurry Heart should be home so let me get her all caught up with what's going on¨

¨I must say seeing this castle never gets old¨ The Doctor said ¨But why could we not have just taken the TARDIS?¨ he said

¨Would you like to explain to my cousin how and why a Blue Box mysteriously transported into the castle?¨ Zap said

¨Duly noted¨ The Doctor said

As Zap approached the door he came to a sudden stop, he then pushed the door slightly and it immediately opened ¨That's strange, Aunt Twilight never leaves the door unlocked¨

¨Derpy stay out here, we dont want any kind of interruptions¨ The Doctor said ¨I have a bad feeling about this¨he said, he and Zap then slowly walked into the castle

Castle of Friendship

¨Flurry?¨ Zap shouted ¨It's me Zap, I came to check up on you!¨ as he walked down the hall he looked in the individual rooms. As he looked around he could see nothing but darkness and a lot of dust.

¨Perhaps Mrs. Sparkle forgot to clean up before she left??¨ The Doctor said, looking around the castle

¨That does not sound like Aunt Twilight at all, she would never leave the castle dirty unless something was wrong¨ Zap explained. As they made there way to the Map Room they noticed the lights where on and the door was cracked open. As the group opened the door they saw Flurry Heart, sitting in Twilight's throne staring at what appears to be the wall from the direction they were standing.

¨Hay Flurry I dont know if you did not hear me or not but I...¨ Zap said before the Doctor put his hoof over his mouth. Then he saw she was not reacting to the group as if she was transfected on something else ¨Uhh, Flurry are you...ok?¨

¨Zap you need to get out of here now¨ Flurry said, her voice sounding concerned ¨Find Celestia and tell her we have a big problem¨

¨Flurry what's wrong¨ Zap said ¨And what are you staring at¨ He then looked in the direction in which Flurry was staring and saw what had her so spooked. Standing in the direction of Flurry was a stone pegasus statue, dressed as a warrior.

¨Uhh Doctor what is that thing?¨ Zap said, however when he turned to look at the doctor he could see the look on his face, the look of pure shock and anger

¨This is impossible, how is there an Angel here?!¨ The Doctor said

¨Doctor im confused what's going on?¨ Zap said

¨That is no ordinary statue¨ The Doctor said ¨Quickly all of you look at the statue and never take your eyes off it, and whatever you do, dont blink¨ He said, then he walked over to the Angel and started to examine it ¨Hmm, it does not appear to be young. It's definitely an older Angel, but how old?¨ He then pulled out his Sonic Screwdriver and began to scan the Angel ¨1,018 years old?!¨ The Doctor said ¨Incredible I had no Idea that you had Weeping Angels...well...Weeping Pegasi in your universe¨

¨Doctor what's it doing here?¨ Zap asked

¨A great question¨ The Doctor said ¨Lets find out shall we?¨

¨And how are we going to do that?¨ Zap said ¨Statues dont exactly talk¨

¨That is true young Zap, however with help from your cousin we should be able to communicate with it¨ The Doctor said, he then turned and looked at Flurry who was still staring at the Angel ¨Hello, my name is The Doctor¨

¨I know¨ Flurry said ¨I have read some of Aunt Twilights reports, your quite the trouble maker apparently¨

¨Well danger and trouble do tend to follow me around¨ The Doctor said ¨Now Flurry, I need you to help me¨

¨How?¨ Flurry said

¨Using your Alicorn Magic, I can make the Weeping Pegasi communicate, however he will be using your voice¨ The Doctor said ¨You will not have any control of your voice, but I am only asking this of you because it is the only way we can find out what its doing here¨

¨How can I be sure it will let me go after we are done?¨ Flurry asked

¨Because if it does not, then it has to deal with me¨ The Doctor said in a stern tone

¨How can I trust you?¨ Flurry said ¨I barely even know you¨

¨Flurry Heart I promise you on my lives, I will not let any harm come to you¨ The Doctor said, he looked at the young Alicorn, while she could not look back Flurry felt something, it was like a mix between Fire and Ice, Rage and Sorrow, somehow in some way, Flurry could tell this pony was trustworthy

¨Doctor¨ Flurry said ¨I trust you¨

¨Thank you¨ The Doctor said ¨All you need to do is perform a telekinetic spell on the Angel and it should start to feed off of the energy allowing us to talk to it¨

As The Doctor has instructed, Flurry lit up her horn and began to use a telekinetic spell on the angel, then as the spell was performed her eyes fell closed and she slumped down

¨Flurry!¨ Zap shouted

¨Do not interrupt the process or we could lose her¨ The Doctor shouted

As Flurys horn continued to glow, Flurys eyes stayed shut however, soon a voice came out that sounded like her, yet it also sounded like somepony else ¨Hello Doctor¨ Flurry said ¨We finally get to see echother again¨

¨Im sorry, have we met before?¨ The Doctor said

¨No, not yet¨ Flurry said ¨But you can call me Angel Bob¨

¨Allright Angel Bob¨ The Doctor said ¨I want to know what your doing here¨

¨I was sent here to remove Twilight Sparkle and her friends from the timeline¨ Angel Bob said ¨After that I was told to remain here and wait for you¨

¨So I was expected then?¨ The Doctor said ¨Who sent you¨

¨I cannot say¨ Angel Bob said ¨But they are an old enemy of yours, when they found me and promised me a way to go home, I took the chance¨

¨Why did they want to get rid of Twilight and her friends what do they have to do with this?¨ The Doctor said

¨Twilight and her friends are to powerful, my master wanted to take them out of the picture so he could deal with you himself, without any kind of issues¨

The Doctor stopped for a moment, he then looked around the room and then back to Angel Bob ¨Did you come alone?¨

¨As always Doctor, you figure our plans out to quickly¨ Angel Bob said ¨No I did not come alone, my partner another enemy of yours, is out looking for you. I have no doubt he will soon try to get your attention¨

Just then Derpy came running into the room in a panic ¨Doctor you have to come to Ponyville there is some creature attacking people¨

¨I see my partner is already doing his work¨ Angel Bob said ¨Do not worry about me Doctor, I was promised that I would go home after I did my job¨ Then he began to glow white, and he slowly started to go transparent ¨Doctor, you must save your friends. He will not stop until you are destroyed¨

¨Who is your master?!¨ The Doctor shouted

¨Not even I know, he only told me he was an enemy of yours, when I asked his name he only said two words¨ Angel Bob said

¨What two words?!¨ The Doctor shouted

¨Bad Wolf¨ Angel Bob said, then he simply just disappeared into thin air leaving the group to themselves. As the group remained in place, taking in what happened Flurry then opens her eyes and slumped back into her chair

¨Flurry!¨ Zap then ran over to her ¨Are you ok?¨

¨Just....a bad headache¨ Flurry said ¨But what about your friend, he seems troubled¨ she said, Zap then looked over at The Doctor, who just continued to stair at what was Angel Bob

¨Bad Wolf¨ The Doctor said ¨How..¨

¨Doctor?¨ Derpy said ¨Please snap out of it, we need to go and save Ponyville¨

¨R-right¨ The Doctor said, he shaked his head a little and looked at the group ¨All Right here is the plan Zap you and Me are going to town and we are going to face this creature. Derpy you need to stay here and look after Flurry¨

¨But I can help to¨ Derpy said

¨Derpy listen I need you to stay here because if we need somepony to look after her, its not a mistake that Twilight and her friends where taken. Whoever this ¨Bad Wolf¨ is knows us and is trying to separate the powerful from the week, if we lose Flurry then things will get worse¨

¨Ok Doctor, I got it¨ Derpy said, she then walked over to Zap and Flurry who was still in her chair ¨Dont worry, I have her. Go and help The Doctor¨

¨Thank you¨ Zap said he then ran to the Doctor ¨Alright let's go save Ponyville¨ Then the two of them ran out the door

Ponyville

As The Doctor and Zap ran into town they could see chaos was everywhere, while not as big as Tireks attack, there where still damages to the town

¨Doctor what do we do, we need to help the ponies still here¨ Zap said

¨Listen Zap, the only way we can help everypony is if we drive this creature out of Ponyville, and if it wants me then its going to get me¨ The Doctor said, the group then walked further into town, but then came to a stop

¨Doctor what's wrong¨ Zap said

¨These houses¨ The Doctor said he walked over to a house and touched the wall, it had a single black scorch mark on it ¨The blaster mark on them, they look like...¨ he said, he then looked around and saw the other houses they all had the same marks ¨No...it cant be...¨ He then ran further into town and stopped when he saw the creature

¨Doctor...what is that thing?¨ Zap said

The creature that stood before the group was a strange metallic being with a dome-like top, an eye that extended like a telescope, several metallic circles on its body, and a suction cup and a strange rod, resembling a stretched egg beater, sticking out from its front chest. It turned its head in a full 180 turn and looked at The Doctor and Zap as if it were looking for something or somepony.

¨YOU ARE THE DOCTOR!!! YOU MUST BE EXTERMINATED!!!¨ The Creature shouted in a loud metallic voice

¨Doctor what is that thing!¨ Zap said ¨And what does it want with you¨

¨Run¨ The Doctor said

¨What?¨ Zap said, confused

¨RUN!!¨ The Doctor said, he then took off and ran in a random direction, Zap doing the same, as he turned around he looked at the creature and it seemed transfixed on The Doctor as it went in the direction he had gone

¨Dang it Doctor!¨ Zap said, he turned around and then ran in the direction The Doctor had gone. As he ran down the pathway he saw more houses that where slightly burning, with single scorch marks on them, as if whatever this creature is was aiming for something, or somepony

¨EXTERMINATE!!¨ The Creature said

¨Doctor!!¨ Zap said he finally found The Creature and The Doctor, who was pinned down in an ally, however the creature then turned its head and looked directly at Zap

¨ALL ALLIES OF THE DOCTOR WILL BE EXTERMINATED!!¨ The Creature said

¨Zap you need to run!!¨ The Doctor said, then The Creature turned its body to Zap

¨EXTERMINATE!!¨ The Creature said, then the strange rod shot a blue beam out of it, and before it could hit Zap, a box was thrown in the direction of the blast distracting the creature

¨Doctor, Zap Run!!!¨ Flurry said

Without asking any questions, and taking advantage of the distraction, The Doctor and Zap ran past the creature and in the direction of Sweet Appledash Acres, with Flurry Heart following behind

Sweet Apple-Dash Acres

As the group made there way to the property they saw that The TARDIS was still in the same place it had been before, catching his breath Zap looked at The Doctor, who himself was slightly pale

¨Doctor what in Celestia's name was that thing?!¨ Zap shouted ¨It almost killed you and me!!¨

¨Its called a Dalek¨ The Doctor said

¨Ok and this Dalek, is it the reason why my Mothers are gone?¨ Zap said

¨No, its only a soldier, I have a feeling however there is more to this than meets the eye¨ The Doctor said

¨Well whatever that thing is, we left it in Ponyville and now we need to go and destroy it!¨ Flurry said

¨No, by now its returned to its master to report on my location, if anything we have a good 2 hours before Ponyville is eradicated¨ The Doctor said

¨But why?!¨ Flurry said ¨We did nothing wrong!!¨

¨As long as I am here everyone in Ponyville is considered an ally of me, and if that's the case then they are just as guilty as me¨ The Doctor said

¨Ok, but we need to at least warn Princess Celestia of the upcoming fight, if we get the Royal Guard then we might stand a chance¨

¨how many ponies are in the Royal Guard?¨ The Doctor said

¨About half a million¨ Flurry said

¨All dead¨ The Doctor said, in a blank tone ¨With one Dalek not even the Royal Guard can survive¨

¨Then how do you suggest we fight the creature?!¨

¨We need to follow the daleks signature and find out who its master is¨ The Doctor said ¨After its master is destroyed hopefully it to will be destroyed¨

¨Well then how do we follow it?¨ Zap said

¨We need to use The TARDIS, its the only thing in Equestria that has the tech to track it¨ The Doctor said, he then looked around and noticed that he was missing one pony ¨Where is Derpy?¨

¨I told her to meet up with me after I found you¨ Flurry said

¨And where is the meating place?¨ The Doctor said

¨Derpy said it was here¨ Flurry said

¨Doctor is she ok??¨ Zap said

¨I dont know, just...let me think!¨ The Doctor shouted, he started to pace back and forth, contemplating on the events of the evening

¨Doctor you dont think The Dalek...¨ Zap said, worried

¨Derpy was not with us when The Dalek first saw us, so she is not considered an ally of me¨ The Doctor said ¨I'm sure wherever Derpy is, she knows what she is doing¨

??????????

¨Hello?¨ Derpy said, she pulled on her hoofs. It seemed they were locked up to something, she could feel metallic chains around them, she looked around the room. It was dark, so she could not see much however she then saw a light and out of the light came a pony shaped figure

¨Well well, looks like the prisoner is up¨ The Pony said

¨Who are you?!¨ Derpy shouted ¨You better let me go, or my friends will...¨ but before she could finish her sentence she started to choke, she could feel something grabbing her neck, she then saw the Pony, who was choking her with his wings

¨Do not worry, I plan on your friends coming. When they do, they along with you will die¨ The Pony said

¨Who...are...you¨ Derpy said, trying to breath from being choked

The Mysterious pony then let Derpy go with his wing and slowly walked to the light again, looking behind him his face became somewhat visible, he had grey fur with a dark black mane, and blue eyes, and he was wearing a green bowtie.

¨You can call me your new master¨ The Pony said, he then walked out of the room, and as the door closed Derpy was now trapped in a pitch black room.

Chapter 4: The Diplomatic Talks

The T.A.R.D.I.S

As Zap, Flurry, and The Doctor enters the TARDIS they made their way to the control panel, The Doctor then pulled some levers and turned a screen in the direction of the two, Zap standing next to Flurry who was still contemplating how she is in a box that is bigger on the Inside.

"Alright, here is what we know" The Doctor said "A Weeping Angel surprised Twilight and her friends at the castle, sending them back in time almost 30 years ago"

"Ok, but what about that Creature from town?" Flurry said

"I'm just getting to that," The Doctor said "We also know that a Dalek, one of my oldest and greatest of foes has somehow found its way to Equestria, and it has been instructed to kill me and my companions"

"But the Angel said that whoever sent the Dalek also sent him" Zap said "He also said that whoever is doing this is an old enemy of yours"

"Precisely, and that my dear Zap is where we now have the upper hand!!" The Doctor said, meanwhile Zap and Flurry just looked at the Doctor, visibly confused as to what exactly he meant "Ugh, what I mean is because this enemy of ours knows me that means he will try to find the T.A.R.D.I.S, and when he or another one of his minions tries to take it"

"We can set a trap!!" Zap said

"Exactly!" The Doctor said

"Ok, but you saw what that Dalek did, how are we supposed to stop it?!" Flurry said

"It's true, you Equestrians don't have the necessary technology to stop a Dalek, however if you know where to go then perhaps instead we can slow it down," The Doctor said, he then walked over to another screen, and pressed some buttons on the control panel, the screen changing images to Canterlot Castle

"We are going to Canterlot?" Zap said

"Yes, and no" The Doctor said "It's true that we can use the Tardis as a trap, however Ponyville is not as protected as Canterlot is, and I cannot have the Tardis fall into the hands of this foe"

"So why go to Canterlot, we would only be putting them in danger with our presence" Zap said

"Because where we are going, only few know about, so much even that Princess Twilight herself does not know about" The Doctor said

"Where is it?" Zap said, now interested by this information

"It's called the Forbidden Section, its located underneath the Canterlot Library and it houses some of the most rarest books and scrolls Equestria has ever seen, the Tardis should be safe while we go and look for some help" The Doctor said

"Wait so we are going to see Celestia and Luna?" Flurry asked

"Yes, right now they need to be informed that something is here, and that something will destroy them if they do not act" The Doctor said

"Well, what are we waiting for??" Zap said "Let's go!"

"I like you Zap" The Doctor said, he then flipped a lever and The Tardis began to make a sound

Canterlot Castle/Throne Room

Celestia sat in her throne, looking over a file she had found in the Museum, a file which should have never been found. As she read the contents, she failed to hear the door open as Luna entered the room.

"Sister, is something troubling you?" Luna said

Startled, Celestia dropped the file, giving out a small yelp from the surprise "Oh my Luna don't sneak up on me like that, you scared me half to death" Celestia said

"We are sorry Sister, we just came by to say we have not gotten any report from Twilight or her friends" Luna said "Usually they would be back by now no?"

"Yes, it is rather odd that they have not checked in," Celestia said, pulling a copy of the note she sent to Twilight out "The instructions were clear, and knowing Twilight she and her friends should have found out what happened by now"

"Sister I have a bad feeling about this" Luna said "Should we send a letter to Spike?"

"I will prepare a letter just in case, until then keep an eye out for her" Celestia said

"As you wish sister" Luna said, she then noticed the file that was on the ground, she could only make out a couple of words within it, but she did indeed see the words King and Maiden, but before she could see any other words Celestia levitated the file close to her and closed it

"Is...that everything?" Celestia said, sounding rather inpatient

"Y.yes" Luna said "I'll go and find the guards to assist in the findings" Luna then turned around and left the room, as she looked behind her she could see Celestia, reading the file

The Restricted Section/Canterlot Public Library

As The Tardis dematerialized in the room The Doctor, Zap, and Flurry stepped out of the police box and began to view the room they had transported into

"Welcome Zap and Flurry, to the Restricted Section" The Doctor said

"Look at all the books here!" Flurry said "Aunt Twilight would have a panic attack if she saw all this" Flurry said

"Ugh...Boring" Zap said "I'm more interested in the Weapons and the Magic Scrolls!"

"My you two do sound a lot like your Parents" The Doctor said, chuckling a bit

"Ok, just take us above so we can find Celestia and Luna" Flurry said

"Hm" The Doctor said "It might not be that easy, no one ever sees you in public Flurry, so we may draw attention to ourselves"

"Then what do you want me to do?" Flurry said

"Well, you can stay here if you want, plenty to read and the Tardis will tell me if anything is wrong"

"You mean you want me, to stay here with all the books from the past that no one, not even Aunt Twilight has read?" Flurry said

"Uh...yes?" The Doctor said, but before he could say anything else a gust of wind flew past him, and Flurry was already tearing apart a bookshelf of books

"That should keep her busy for a good few hours" The Doctor said "Now Zap come on, we need to get the Princess's"

"Alright let's go" Zap said

Canterlot Castle/Lunas Room

Luna sat in her chair, thinking. Celestia was definitely acting weird, first she does not know the whereabouts of her own pupil, and she is also keeping something from her regarding the file. However she had more important things to worry about, Twilight and her friends were still missing and she needed to find out what happened to them.

"Your Majesty" A Night Guard said "You wanted to see me?"

"Yes, I need you to do me a favor" Luna said

"What is it?" The Guard asked

"I'm going to give you a mission, however I do not want you to report this to your Captain, this is strictly off the books" Luna said

"As you wish Princess, what is the mission?" The Guard said

"I want you to report to me the routine of Celestia, where she goes, what she does and more importantly if she is hiding anything" Luna said

"If I may ask Princess, is this not technically spying against the crown?" The Guard asked, concern in his voice

"Yes, however I only ask this because I want to keep my sister and myselfs position safe, if Celestia is hiding something, and somehow it leaks then not only myself, but Celestia's trust with the public will be compromised" Luna said

"I understand Princess Luna" The Guard said

"If you find anything that is urgent, report to me at once, do not tell anyone where you are going, just leave and don't say why" Luna said "if Ponies ask what you're doing, tell them your running errands for me"

"Yes Princess" The Guard said, he then turned and walked out the door leaving Luna to her thoughts

"What are you hiding sister..." Luna thought "And why do I have the feeling, it is something that can mean the jeopardy of the land itself"

Canterlot

As The Doctor stood in the streets of the city, he took out his Sonic Screwdriver and began scanning the area. Ever since they had left the Restricted Section he had been fiddling with the device, it seemed that he was looking for something, but Zap was not exactly sure what he was looking for.

"Doctor come on, we need to get going!" Zap said

"What?" The Doctor said. he then turned around and remembered what they where doing "Ah yes, the Castle right"

"Doctor what are you doing?, you have been playing with that thing for a while now" Zap curiously then looked around the area, as they continued to walk the streets.

"I'm just looking for something" The Doctor said

"Doctor my mother is the element of honesty, even if she was not here I can tell your hiding something" Zap said, his face slightly pouting

"I'm looking for Derpy" The Doctor said

"Why? she should be in Ponyville still right?" Zap asked

"Yes, however with the Dalek around I can never be too safe" The Doctor said "I gave her a piece of jewelry a while back, the gem located in it is essay trackable, so theoretically I should be able to know where she is. However for some reason its not showing up"

"That is wired" Zap said "You dont think she is in any kind of danger do you?"

"Thats what im worried about" The Doctor said, his tone slightly flat.

As the group came to the castle entrance they were then stopped by two guards "Hult!" One of the guards said

"Who goes there?" The Other guard said, both the guards wings where blocking the path, there gazes locked on the two ponies

"Hello there, my name is The Doctor, i'm here to see Princess Celestia or Luna" The Doctor said

"Do you have an appointment with them?" the Guard said, his brow raising a bit

"Uh, no I just need to speak with them" The Doctor said

"If you dont have an appointment then you cannot enter" The Guard said

"Listen its really important that we see Princess Celestia!" Zap said "The fate of equestria is at stake!"

"Sure kid" The Guard said

"Ugh I dont have time for this" The Doctor mumbled, he then pulled out a piece of cloth and opened it, showing it to the guards "I believe this is enough proof"

The guard looked at the paper, his eyes going wide a bit he signed to the other guard to put his wings down "My apologies Sir Doctor"

"Thank you" The Doctor said, he then walked past them Zap nervously following behind him

Castle Hallway

As Zap and The Doctor made there way down the hall, Zap looked at the scenery. He looked around the marvels of structure, taking in every single detail of it. The window art depicting his Mothers and there many adventures, the defeat of Discord, the great Shadowbolt Battle, and many other things.

"Hay Doctor, what did you show to the two guards?" Zap asked "It made them look like they just peed themselves"

"Its called Physic Paper, it shows weak minded people whatever they or I want them to see" The Doctor said "When the guard looked at it he saw an ID for the royal guard inspection officer"

"So that only works on week minded people?" Zap asked "What about the smart people?"

"They will see only a blank sheet of paper" The Doctor said, as the two ponies continued to walk down the hallway they could make out one of the Princess

"Princess Luna!" Zap said

Hearing her name Luna turned to see the two ponies, one of which she recognized "Doctor?" Luna asked

"Hello again Princess" The Doctor said "I'm sorry to barge in but I need to speak with you and Celestia, it's about Twilight"

"You know where she is?" Luna asked "I have been trying to contact her all day, is she ok?"

"All will be explained in time, just find Celestia and met me in the Throne Room"

"If you say so Doctor" Luna said, she then turned around from the direction she was going, and ran to Celestia's room

Castle Throne Room

"Thank you so much for seeing me Princess Celestia and Luna" The Doctor said "Again I would like to apologize my unannounced visit but the matter is dire"

"It is fine Doctor, now you had told my sister you know what happened to Twilight and her friends?" Celestia said

"Yes, i'm afraid a creature known as a Weeping Angel somehow found them, and transported them 30 years into the past" The Doctor said

"How is that possible?" Celestia said

"The Weeping Angels feed off of the lives that could have been when they transport ponies back in time" The Doctor said "However there is a more concerning matter at hand"

"You mean there is more to this?" Luna asked

"Yes, the Weeping Angel was not working alone, he along with an old foe of mine are working for somepony who wishes to have me destroyed, and possibly take over Equestria"

"If what you say is true then we need to rally up the troops and locate this menace" Celestia said "We cannot have a repeat of Tireks invasion"

"Siester, Equestria has been at peace for 10 months, and much of the country is still rebuilding itself" Luna said "Are you sure gathering the army is the best decision?"

"What else do you suggest we do Sister?" Celestia said in a stern tone

"We could try to reason with the pony" Luna said "We can just send an army to whatever threat comes our way, there has to be a diplomatic solution!" Luna said, slightly shouting

"Luna I out of all ponies know when the time is needed for diplomatic talks, and now is not the time!" Celestia said shouting

"Hoofs On Muzzles!!!" The Doctor shouted, and as if by magic Luna and Celestia put there hoofs on there muzzles and stopped talking "Now, before you two start to argue again, I am more concerned about another ordeal, I previously said that an old foe of mine was working with the pony who wants me dead, this foe is like none you will ever face and if you dont destroy it then Equestria will burn"

"What do you mean burn?" Luna asked, slightly worried

"I mean it will literally be burned, gone, reduced to atoms" The Doctor said "This enemy only knows one thing, and that the extermination of all living things"

"Then what preatell do you suggest we do Doctor" Celestia said

"I need your best soldiers to go and protect the Canterlot Public Library" The Doctor said

"Why there?" Celestia asked

"I put my Tardis in the Restricted Section, if this enemy gets a hold of it, then we truly have lost" The Doctor said

"We...will get our best soldiers on it" Celestia said

"And make sure that its discreet, if a bunch of soldiers just show up in front of the library then it will look suspicious" The Doctor said "So have them spread out but only to where they can see the library and all of its entirety"

"And what about the Restricted Section?" Luna said

"Flurry Heart is down there with my Tardis, she should be safe as long as she does not leave the room" The Doctor said

"If you say so Doctor" Celestia said

"Thank you for your time Princess, now if you would excuse me" The Doctor turned around and began to walk out the room before he was stopped

"Doctor, when you find this threat, I want him destroyed" Celestia said, The Doctor turned around to see her as well as a surprised Luna

"Sister you cannot be.." Luna said before she was cut off

"If this pony is as dangerous as you think he is, then he must not be allowed to remain alive" Celestia said

"If...you say so Princess Celestia" The Doctor turned around and walked out the door. Zap who had been waiting outside the room started to follow the doctor as they went to leave the castle

"Doctor, what's wrong?" Zap said "You seem troubled

"Celestia is acting weird, she was never this assertive when I last knew her and she certainly would not want a pony destroyed all it be even as a last resort" The Doctor said

"Do you think she is not the real Celestia?" Zap said quietly as to not have anyone else hear him

"No, she is real I could feel it" The Doctor said "But something is definitely up with her"

"So what do you suggest we do?" Zap asked

"I'm afraid at the moment we have a greater concern" The Doctor said "However Celestia keeps acting the ways she is I fear that the golden age of Equestria may come to an end"

Author's Note

Hay guys I'm not Dead!!!! hopefully you guys enjoyed this chapter, sorry for the long wait. Hopefully the next chapter will not take as long as this one did

Chapter 5: The Good, The Bad, And The Discorded

????

As Derpy hung on the wall, she tried to make out a plan. While this was not the first time she was captured, she usually had company with her, so for now she was on her own.

"Think Derpy, what would The Doctor do?" Derpy thought to herself, as she wiggled her chains around she tried to feel for any kind of weakness in the wall, perhaps she could pull the chains out if they got enough momentum from flying in one direction. As she began to tug on the chain she could hear something coming down the hall, it was a loud clanking noise, it had to be made of metal by the sound of it alone. The door then opens and her Ceptor came in followed by two Silver Robotic Ponies with glowing blue eyes

"Well well, looks like Mrs. Doo is trying to escape" The Pony said, his voice brash yet, somehow familiar

"What do you want with me!" Derpy shouted

"Nothing, as of yet" The Pony said "Your merely a piece to a large puzzle in the works"

"What do you mean?" Derpy said

"All will be revealed in time Mrs. Doo" The Pony said "But for now I need something of yours"

"And what exactly would that be?" Derpy said, nervously questioning her captor

The Pony then held his hoof out and reached to Derpy's neck, he then grabbed the gold necklace she was wearing "Such a nice piece of jewelry" The Pony said, he then took something from out of his pocket, when some light hit the room, Derpy was surprised to see what looked like The Doctors own Sonic Screwdriver, only it looked like it had been burnt in a fire, as the silver was more black, and the blue tip had a crack in it

"What do you want with my Necklace?" Derpy said

"Oh it's not the necklace itself, rather the jewel in the center of it" The Pony said, he then pointed the Sonic at the Necklaces Gem and turned it on, causing the necklace to pulse green

"What did you do?!" Derpy said

"I merely just called an old friend" The Pony said, he then walked away and the two Robotic Ponies followed him, yet again leaving Derpy alone.

Canterlot

As Zap and The Doctor walked down the street, The Doctor kept thinking back to Celestia. She was never this assertive to Luna or Him in the past, furthermore she had never directly told somepony to kill another. Something was definitely up with her, however he hadn't the slightest of what it was.

¨Doctor I have a question¨ Zap asked

¨Yes, what is it?¨ The Doctor said, snapping out of his thoughts

¨Why have we not gone back in time and rescued my parents¨ Zap asked, his tone a mix of sadness and anger

¨Well, you see its quite complicated¨ The Doctor said, trying to move away from the topic

¨Doctor, I want to know¨ Zap said, his tone becoming more stern¨

The Doctor sighed and he grabbed his screwdriver to fidget with ¨You see Zap, time is like one big ball of wibbly-wobbly timey wimey...stuff¨ The Doctor explained ¨When the Weeping Angel sent your Twilight and your Parents back in time, they indirectly made them a part of history, somehow in some way your parents have become a part of history, and if they were still stuck in the past until they passed then we would know about it. After all we don't see any gravestones of them, which means that they came back somehow. However according to Twilight in her letter, they ran into a version of myself from the future and my future self told them that they could not come back until the time is right.¨

¨So what you're saying is that until the future version of yourself brings my parents and Twilight back, they are stuck in the past¨ Zap said, disappointment in his face

¨Don't worry Zap, if my future self is with them then they are safe¨ The Doctor said ¨Now, we should probably head back to the Tardis to let flurry heart know that we found Celestia and Luna..¨

But before The Doctor could finish his sentence, his sonic began to pulse blue. He held up the screwdriver and began to smirk ¨Its working!¨ he shouted

¨Uh, what's working Doctor?¨ Zap said

¨Derpy's tracker, it just came online!¨ The Doctor shouted in excitement

¨Well then where is she?¨ Zap asked

¨Well you see it's not like that, the Screwdriver is like a beacon. The brighter it glows means we are going in the right direction¨ The Doctor explained, he then looked at his screwdriver to observe the glow of the light ¨By the looks of thing she is in Canterlot, however she is not close to our location¨

¨Well then what are we waiting for?! let's go!!¨ Zap said

¨I'm liking you more and more Zap Apple¨ The Doctor smirked ¨Alonz-y!!¨

Canterlot Warehouse District

¨Why is it that all my adversaries insist on making there secret headquarters in Warehouses, it's so cleshay¨ The Doctor said ¨Why not make it more exciting, like a Spaceship over the planet! Or hell, another planet!¨

"Doctor, focus" Zap said "What does your Screwdriver say now?"

"Oh right" The Doctor said, he then looked at his screwdriver and moved around, making sure the direction in which he was going, the light got brighter. Then, the blue light started to glow brighter when he held it at a Warehouse marked N5 "I think we just found the area."

"Warehouse N5" Zap said "Why would Derpy be here?"

"Well think Zap, derpy would not consciously come here for no reason, obviously she has been captured, I'm surprised you did not catch on before hoof" The Doctor said "Anyway, whoever took Derpy obviously wanted to meet here so, that's why we are here."

"This is definitely a trap" Zap said "I can feel it."

"Oh most definitely it is a trap" The Doctor said.

"So...what do we do?" Zap said.

"We spring the trap" The Doctor said, smirking a bit. He then walked up to the Warehouse and pushed on the giant wooden door, as he looked inside he could see that this Warehouse was clearly bigger than he thought it was, he could see multiple doorways, leading to many different rooms, of which Derpy could be located in.

"This is one big Warehouse" Zap said

"For some reason...this place feels...familiar" The Doctor said.

"Familiar in a good way?" Zap asked.

"I dont know, I can't put my hoof on it" The Doctor said. As they looked around the room, more of the details could be seen. The walls and floor of the Warehouse were made of a type of metal, and the lights in the room were dimly lit, suggesting no one has been in here for quite some time.

"Doctor, this place looks huge, how are we going to find Derpy?" Zap said.

The Doctor looked at his Sonic, it was not pulsing blue, which meant they could not rely on the necklace anymore, he then looked around the room, taking note of each doorway "Well I'm afraid to say I don't exactly know what to do" The Doctor said "At most, we just have to look around and hopefully whatever or whoever took derpy will show itself."

"What makes you so certain that will happen?" Zap asked.

"Because knowing my enemies, they would want to make sure I know who did the thing they are planning on doing" The Doctor said.

"You have a lot of enemies that think highly of themselves" Zap said bluntly.

"You have no idea" The Doctor said. As the two ponies looked around the room more, Zap then saw what appeared to be a control panel, it was round in structure and it seemed to have a tube coming from the middle of it, the tube was covered in cracks and the glass was all dirty. He looked down at the control panel and saw that the panel was in no better shape, buttons were missing and levers were broken.

"Hay Doctor" Zap said "I think I found something."

As The Doctor traveled over to Zap he started to slow down, noticing the same things Zap did he quickly searched the area, looking at the room. He then went over to the control panel and lightly caressed it, his eyes slightly drooping, and his mouth frowning a bit.

"What have they done to you" The Doctor said.

"Doctor?" Zap said "What's wrong."

"Don't you see?" The Doctor said, his voice getting slightly angry "This was a TARDIS, not just any TARDIS" The Doctor stopped, he then went over to a hole in the control panel, he then took out his Sonic Screwdriver and placed it in there, sliding in almost perfectly "This was My TARDIS" The Doctor said.

"That it was....your TARDIS" A voice came out from behind the two ponies, The Doctor and Zap turned over to see a Grey Pegasus before them, he had a black mane, and his eyes were a dark blue, with wrinkles under them, suggesting stress or anger. He was wearing a green bow tie and had the same cutie mark as The Doctor "Or should I say, our TARDIS" The Pony said.

"Doctor?" Zap said "Why does he look like...."

"Why do I look like him?" The Pony replied "Well dear Zap, it's because I am him" He then walked over to the Doctor and held up his Sonic Screwdriver, The Doctor then pulled out his, they were the same device.

"You can't be..." The Doctor said.

"Allow me to introduce myself" The Pony said "Hello, I am The Doctor" he said, with an evil, malicious-like grin.

As the two Doctors stood across from one another, millions of questions rolled through Zap's mind. How can there be two Doctors? How are they in The TARDIS, it does not look like it. "I don't understand" Zap finally spoke "How can you be The Doctor, you don't even look like him"

"Oh trust me, I am The Doctor," he said "I'm just not the one you are with right now"

"That still does not answer my question," Zap said

"Zap, when Time Lords die, we regenerate our bodies, it like a way of cheating death. However in the process of Regeneration, we change bodies, personalities, and faces" The Doctor said "Only this version of me, is not right"

"Oh trust me when I say, it is in fact you who are not right my dear Doctor" The Other Doctor stated

"Why would we do this to ourselves?!" The Doctor demanded "You kidnap our companion, gut the TARDIS for scraps!?"

"You will do the same in time Doctor!" The Other Doctor shouted "I am not just you, but the you from the future, a future in which all of this will happen"

"I would never become something as vile as you," The Doctor said

"You say that now" The Other Doctor said "But in time, you will become me, and when you do everything will make sense"

"Make sense?!" The Doctor shouted "You decided to bring back not only The Daleks, but The Weeping Angels, and The Cybermen all to make a bloody point?!"

"I'm doing all of this to prevent a catastrophe Doctor!" The Other Doctor said "I saw the truth! the truth that was hidden from all of us for centuries!"

"What truth?" The Doctor said

"The Truth about us Doctor, why we are here in this place" The Other Doctor said "An ancient evil is at works in this land, and it's unlike anything we have ever faced before, I am doing what you cant! ending all of it before it can even begin!"

"What do you mean ending all of it?" Zap said

"Oh, I'm glad you asked" The Other Doctor said, he then activated his sonic, and the entire building began to shake, as the floor then began to open revealing a giant red and black machine covered in wires and alien crystals. In the center of the machine was a strange Dark Blue item, in the center of it was a depiction of an eye.

"No, it can't be" The Doctor said

"Oh so you do recognize it!" The Other Doctor said

"Doctor what is that thing?!" Zap said

"It's a paradox machine" The Doctor said

"I borrowed the idea from our good friend The Master" The Other Doctor said "Oh you remember that day, giant rips through dimensions, one-third of the population of the earth being destroyed, such a lovely day"

"What's it for? What does a paradox machine do?" Zap said "More important, can you stop it?"

"Not till I know what it's doing. Touch the wrong bit, blow up the solar system." The Doctor said

"But you said you have dealt with this before, so why not do the same thing as last time!" Zap asked

"Because last time it was not me who made the machine, different mind, different purpose" The Doctor said

"Oh, we are so clever" The Other Doctor said "I might as well just say my entire plan, allowing you to figure out a way to stop me"

"Look at what you are doing!" The Doctor said "This is not us! we took an oath, never to become something like this!"

"Screw the oath, and screw the Time Lords!" The Other Doctor said "Compared to us Doctor, they are like ants, and we are a boot"

"I'm warning you!" The Doctor said

"Oh and I'm warning you Doctor!" The Other Doctor said "Don't mess with me, I'm not like The master, or any of our other adversaries, I'm so much more" He then pointed to one of the doorways, coming out of the doorway was Two Cyber Ponies holding Derpy by the hooves, not letting her go

"Doctor!" Derpy said "Doctor listen don't worry about me, deal with the problem at hand. I can handle myself!¨

¨No don't please!¨ The Doctor shouted ¨She has nothing to do with this leave her out of it!¨

¨There he goes again, with the saving and the life is precious speech¨ The Other Doctor said ¨Doesn't it ever get old saying the same bloody thing over and over again!¨

¨Let her go!¨ The Doctor shouted

“No I don't think I will” The other doctor said “Now doctor, allow me to demonstrate what my new and improved paradox machine can do!” The Other Doctor then looked at a Cyber Pony “You! Step over here, now!”

The Cyberpony then stepped forward and stood on what looked like a red circle marked next to the Tardis Control Module

“You see Doctor, I realized that if I want to stop the future from happening, I merely need to stop the future entirely! So using some Z-neutrino energy, as well as the magic within this world as a Single string Z-neutrinos compression”

“No!! you can't! You can't! No!” The Doctor who cried out

“Oh yes...I was able to create….a reality bomb...using the TARDIS as a power source.” The Other Doctor said

“But...I don't understand, what does he mean by Reality Bomb?!” Zap said”

“Electrical energy, Zap. Every atom in existence is bound by an electrical field. The Reality bomb cancels it out. The structure falls apart” The Other Doctor said, then he flipped a lever on the Tardis counsel “Allow me to demonstrate...”

As soon as the lever was flipped, the Cyberpony began to slowly disappear, as his entire body floated in the air, and his feet, body, and finally head completely turned to nothing “You see Zap? And with this Reality Bomb, Ponies all across Equestria will bein to turn to dust!”

“The Missing Ponies! You're behind them?!” The Doctor said

“Yes, after all I needed some way to test this machine out” The Other Doctor said with a wicked smile “And soon after that? I will use the machine on planets and stars! And they will become dust, and the dust will become atoms, and the atoms will become nothing. And the wavelength will continue, breaking through the Rift at the heart of the Medusa Cascade into every dimension, every parallel, every single corner of creation. This is my plan, Doctor! The destruction of reality itself!”

“Your mad!!” The Doctor said

“You mean, we..Doctor” The Other Doctor said

¨Doctor we have to do something!!¨ Zap shouted

¨Yes doctor! do something after all, you always save the day¨ The Other Doctor shouted

The Doctor thought a million things at once, so many things but he could not think of anything. Nothing came to mind he was out of ideas, for once he may not win this battle.

Chapter 6: The Long Way Round

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