The Doctor and Twilight Sparkle: The Day Equestria Cried Doctor

by TheMasterBronyDoctorGuy

Rating: everyone
Tags: Comedy, Adventure, Crossover, Alternate Universe
Length: 14528

The Doctor has appeared in a troubled time in Equestria. With the help of Twilight Sparkle and Derpy Hooves they will fnd out the problems solution

The Doctor had been to Equetria before but he hadn't been there long. Now he returns finding a destroyed Equestria under the rule of Tirek. The Doctor goes to find the companion he knows best in Equestria. Will the Doctor and his companions stop the darkness in which he has been sent to defeat?

Published 1970-01-01 00:00:00 UTC
Last updated 2014-10-02 10:11:43 UTC

The Prologue

A being quickly runs through corridors trying to find what it was looking for. It had checked every single room. All but one that was the library. *Flick*.

"There you are," the being said. This being was a lavender alicorn with a blackish mane and tail with the occasional pink and grey stripes. She had been looking for a book that she had been told to hold onto. It was called the TARDIS Manual. The Doctor had given Twilight the book to look over for the next time he came to Equestria. He promised to show her the universe and alternate dimensions. She could still remember the day.

"Doctor," Twilight yelled chasing after the chestnut stallion.

"Yes?" Doctor Whooves asked

"When will you be back," Twilight said expecting soon to be his answer.

"I don't know Twilight but I promise next time I won't leave without you." He went inside the TARDIS and came out with a large blue covered book. He blew on it and it caused a lot of dust to fly.

"You're gonna want to read this," he said.

"I thought I had lost you," Twilight Sparkle said returning to the present, " Spike!"

"Yeah," Spike said.

"Please put this book in the chest in front of my bed," Twilight said. It had been a whole year since The Doctor's last visit. She went and got a drink of water. She then went upsatairs and said goodnight to everyone, went to her room and fell asleep. Her dreams wouldn't last long as she was to have an unexpected visitor.

We find our googly eyed pony delivering her last piece of mail of the day.

"Thank you for allowing me to deliver your mail," she said doing what her boss told her to.

"Thanks Derpy," said a unicorn who had decided to settle down early and watch some tv.  It was obviouse because the whole room smelt of popcorn and the unicorn had dressed in pajamas. Derpy flew off heading back to the post office. When she saw him he was waiting outside Canterlot next to his blue box the Tardis. Derpy literally flew down and tackled him.

"Hey Doctor what brings you back to Equestria?" Derpy asked with a smile with the words sorry painted all over it. The Doctor got back up before speaking.

"Well i'm here because, well frankly I really don't know why I'm here." The Doctor said.

"Well its good to see you again Doc. Why don't you head over to my place while I go return these saddlebags to the post office," she said hoping for him to say yes.

"I'm sorry Derpy but i'm not here for a reunion," he said. That was a lie you came here to see Twilight, he said to himself.

"Oh um, thats okay but it was great to see you again," she said looking quite upset.

"Good bye Derpy," he said. Derpy flew off she was quite upset knowing that the Doctor wasn't going to be here long. She returned the saddlebags and went home.

Twilight awoke to a knocking at the door. The sun hadn't risen yet so she was wondering who would be stopping by at this hour. She got out a lantern and walked to the door.

"Who is it?" she asked.

"Actually, I don't know do you," Doctor said. Twilight's ears perked up and she regained a lot of energy.

"Doctor?" She asked.

"No who else would come to you at the most unreasonable of times," he said sarcastically. Twilight quickly opened the door with her magic almost ripping the door off its hinges. There stood The Doctor the chestnut colored stallion she had met only a year ago.

"I'm going to take that as an invitation inside" he asked.

"Come on in," Twilight said as she blushed from embarrassment. They both sat down in what was the dining room. The walls were made of crystal and the cabinets of the strongest wood out there. There was an oven sitting next to a sink they were both made of the finest metal. The fridge was on the the left when you walked into the room and there was a window over looking a beautiful lake. Twilight quickly made some tea. Then there came trotting from the stairs and down came a half asleep Applejack.

"Twi it's too early in the mornin ta be making tea," she said looking around. She then noticed The Doctor. "Now who's this handsome stallion," she said looking at him from head to hoof.

"This is my friend the Doctor ," Twilight said in response.

"Well he sure is handsome," Applejack said.

"You already said that, um whats her name?" he asked.

"Doctor this is Applejack," she said angrily.

"You already said that Applejack," Doctor said," and you are making me feel uncomfortable." Applejack then and went to get everyone else. While she was gone they continued their conversation.

"Last time I was here you had a treehouse now a castle and wings. Wow I must have been gone pretty long then," he said as he looked around.

"Yeah, its a long story. I wish I could tell you but Applejack and everypony will be here quite..." she stopped to indicate the sound of twelve hooves trotting down the stairs and the slight sound of wings batting. The first to enter was Rarity, followed by Fluttershy. Next came Applejack, followed by Pinkie Pie, and then Rainbow Dash. All but Rainbow's and Applejacks's mouths dropped

"My you were right Applejack he is handsome," Rarity said.

"I don't know if I would call him handsome," Rainbow Dash said.

"Now Rainbow Dash no need to be rude," Rarity said. Rainbow Dash just gave a puzzled look and looked back towards Twilight and The Doctor.

"Can you guys leave us for a bit," Twilight asked as politely as possible. They all nodded their heads and trotted off back to their rooms.

"Now where was I before we were so rudely interrupted  by those 5, I was going to ask if you still wanted to come with me on....." befor he could finish Twilight had already bolted off towards her room.

When Twilight arrived In her room she wrote a note to Celestia saying the following:

Dear Princess Celestia,

I Twilight Sparkle am leaving with The Doctor to travel the universe and to other dimensions. It may be years before I return so please take care of Spike while i'm gone.

Your faithful student,

Twilight Sparkle

Twilight packed her things and went to meet The Doctor downstairs.

"Then lets go shall we there are whole dimensions to see and universes to adore..." The Doctor talked on and on about the universes Twilight was about to see.

"Ladies first," he said opening the door for Twilight. She set her stuff near a chair and sat down.

"Now when we leave your body will shift from alicorn to human," he said as he started up the TARDIS.

"Oh i've been there, I know how it feels," she said thinking back to her time at Canterlot High in the human world she had been to.

"Then lets start hitting the time stream," he said pushing buttons. He pulled a lever and the TARDIS shook. "You are about to see whole universes in hours,"  he said smiling.

Chapter 1: The Darkness was Unleashed

It had been two whole years since Twilight was in equestria. The Doctor and Twilight sat in some chairs talking about their most recent adventures. Twilight's appearance had changed a bit since her transformation from aliicorn to human. She had become quite accustomed to human anatomy than her own alicorn anatomy. Her hair had been given a little glow or sparkle. She was wearing reading glasses as she had been given this defect through her transformation. She had a pair of boots with high heels on as she had also grown accustomed to this change. She also wanted to feel like she was still trotting around. She wore jeans with a light t-shirt over top that said Twilightliciouse and it showed herself on the shirt.

"Now where was I, oh yes and can you still believe we did this in two years equestria time," he said laughing at the most recent conundrum that occured. Twilight looked up from her book and gave him a smile she still didn't understand the Doctor's humor.

"Well where are we headed now," Twilight asked.

"We're going to visit an old equine friend of mine," The Doctor said.

"Who is this other equine," she said.

"Oh her name is Derpy and she is quite the interesting gal, er I mean friend,"  he said stuttering.

Twilight shrugged and went back to her book. She was ready to get used to her wings and magic again. She just didn't know how much she had missed while she was away. Did her friends even know she existed anymore. As they entered the apparently named My Little Pony: Friendship is Magic dimension she started to change from human to alicorn once again. First her muzzle formed and her hands became hooves. Her tail started to form along with her horn and wings she eventually was a pony again. They left the TARDIS to find Canterlot in ruins the royal castle looked abandoned and the streets were as well. Buildings lay in ruin and smoke rose above Canterlot putting it into a shroud of darkness.

"Oh my, what happened here," Doctor said looking around.

"I have to find Celestia," Twilight said teleporting away. Inside the castle wasn't any better than outside. The stained windows were shattered and some marble columns were cracked and broken. She found the throne room to see that on the throne sat Tirek and next to him sat in chains Celestia, Luna, and Cadence.

Tirek quickly rose to his feet laughing, "hahahahaha, so she returns the princess of friendship," Tirek knocked a pillar down causing part of the room to collapse.

"What happened," she asked.

"I took over equestria thats what happened," Tirek said stepping closer every second.

"Where are my friends," she asked hoping for the best.

"You mean them," he turned around and pointed at 4 mares who obviously weren't themselves. Rainbow Dash now had scars and a broken wing. Pinkie pie's hair had been buzz cut and she looked quite angry. Rarity now had no horn it had been torn off. Applejack now wore armor and at her side was a sword, and Fluttershy was nowhere to be seen.

"What did you do to them," Twilight stomped her foot in anger.

"I took away their magic. What did you call it, oh yes the magic of friendship," Tirek laughed, "I convinced them that you were never coming back and they kneeled before me. I took their magic and they all became distant and now can't stand to be near each other." As if on que Rainbow kicked Applejack in the side.

"And now Twilight Sparkle join your princesses as my pet," he said opening his mouth to absorb her magic. She quickly teleported to get away. She remembered that The Doctor had decided to head to cloudsdale. Twilight then flew off to find the Doctor.

Chapter 2: Finding Derpy

"Derpy, Derpy!" yelled The Doctor. He had been galloping through the destroyed streets of Cloudsdale looking for her. Then Twilight landed in front of him.

"Stop calling her name she can't hear you," she said.

"Why," the Doctor looked concerned.

"Because, because Tirek drained her pegasus magic," she said upset. "She can't hear you because she is down on the ground, not in Cloudsdale."

"Then we need to get her," he said. He turned around to leave but Twilight stopped him.

"I can't be seen in public Tirek is on the loose he caused this I have to stay out of sight for the time being," Twilight said," come get me once you find her i'll be in the TARDIS." She trotted off so she wouldn't get any attention from above.

The Doctor had been all over Ponyville the streets looked old and faded some houses were either under construction or were in a complete waist."Derpy, excuse me have you seen a grey pegasus with a blonde mane?" the Doctor asked a gloomy looking stallion.

"No I haven't now buck off," the angry stallion said.

"Derpy, where are you," he called out looking around. Then he saw her sitting at a table near what used to be Sugar Cube Corner.

"Derpy, Derpy over here!" he yelled running through the crowd of ponies. Derpy looked in his direction and slowly looked away. When he got there he was at least expecting a smile on her face but instead she said.

"Oh its you." Derpy chucked a muffin at The Doctor.

"Derpy whats wrong why are you so angry at me," the Doctor asked.

"Because you left without me. You said we were friends and you left me," she said with a tear rolling down her cheek.

"Oh, Derpy we've been through this I wasn't there for you to come with," he said trying not to tell her the truth.

"I was there because the TARDIS was on the frits." He smiled hoping to see her cheer up a bit.

"She just looked so appealing didn't she," Derpy said pointing at a sign. The sign said:

WANTED

Princess Twilight Sparkle

130,000,000 bits

Fluttershy

180,000 bits

Discord

200,000,000 bits

Each of them had a picture under the names.

"How did you know that?" he asked.

"I saw you enter the TARDIS with her, you were laughing and talking about the adventures you were going to go on," she said shedding another tear.

"Now Derpy," he said sitting next to her," I promised Twilight Sparkle I would show her the universe."

"Well maybe I wanted to see it to," she said scooting over to the other bench.

"Derpy, you know I would never try to hurt you in anyway," he said once again hoping she wpuld forgive him.

"Well you did you hurt me right here," she said pointing at her heart. At the start of the streat there was screaming. There standing was an armor clad Rainbow Dash. She snorted looking around for Twilight Sparkle. Her magic detector had picked up magic in the area and she was going to find it.

"We can talk about this later, but right now we have to get to the TARDIS," at the mentioning of the TARDIS Derpy jumped up and said," so I am going to get to see the universe," she said excitedly.

"Yes, but we need to go now," he said with urgency.

"Okay," she said. They then slipped into an alleyway.

Chapter 3: Through the alleyways

"Hurry Derpy," Doctor said.

"What me and Rainbow are friends," Derpy said.

"Not anymore Derpy, nopony is your friend, nopony but me," he said turning his head and smiling. He had noticed that the rainbow maned pegasus, she'd ask Twilight for her name later, had a broken wing she wouldn't be able to catch up to them as long as they kept running. They made it to an alleyway with a gate on the side.

"Stop in the name of the T.D.F.," Rainbow Dash yelled. She had somehow made it in front of them.

"No," he said pulling out his sonic screwdriver. He aimed it at the locked gate and pressed the button. With a whirring noise the screwdriver found its mark and the lock dropped to the ground. He shoved Derpy into the gate to open it and then he ran in after her.

"He's the one emitting the magic he must know where Princess Twilight is," she said talking into a communication device.

"Good you must lose the armor and the sword," Tirek said. "Tell them that T.D.F stands for, Tirek Defeat Force and gain their trust."

"Yes, Lord Tirek," Rainbow said.

"Why would she do that," Twilight said trotting around the TARDIS. "Why would Rainbow attack you."

"She yelled at us in the name of the T.D.F." the Doctor said. He didn't know what it stood for but it didn't sound good.

"Well it could have mean't anything," Derpy said.

"Yes Derpy it could have," The Doctor said. Then there was a knocking at the TARDIS door.

"Well thats strange it's 11:00 at night. And I don't think anyone knows we're here." The Doctor said.

"Derpy please check the door?" Twilight asked.

"Sure thing," she said glaring at Twilight. She opened the door and screamed. There at the door was Rainbow Dash.

"Rainbow Dash," Twilight yelled in surprise.

"Hey T..." she didn't even finish her sentence.

"You," the Doctor yelled. "What are you doing here." Rainbow looked around.

"Well I can see you're busy with these guys so..." once again interrupted.

"No please come in," Twilight said. She gave The Doctor a look.

"Thanks," she said quickly moving through the door way. This was Rainbow's first look at the TARDIS from the inside. From the outside she thought it was very cramped but she was quite wrong. The middle had a command station with buttons and switches galore. It had been a while and the Doctor was constantly asking questions.

"What does T.D.F. stand for," he asked

"It stands for Tirek defeat force," she said without stuttering.

"Doctor stop asking her all these questions she isn't here to hurt us," Twilight said.

"Fine," he said unsatisfied. It was quiet for a while then Rainbow started asking questions.

"So, do you know how long you were gone," she asked.

"Two years," Twilight said.

"Why did you leave so long," Rainbow asked.

"Because I thought you could handle a little time without me," she said. "But I guess I was wrong."

"Sure to hay you were," Rainbow said.

"I know that now Rainbow but I didn't expect to be gone for two years," she said looking away so she couldn't see Rainbow's angry face.

"Whats that," she said pointing at the clothes Twilight had been wearing.

"Oh it's nothing important," she said blushing.

"Well they look pretty weird," she said tilting her head. It was quiet for a little longer then Twilight asked.

"Rainbow I need your help," she said.

"Why?" Rainbow asked

"Because, I need you to help me get into the castle and stop Tirek," Twilight said.

"I only know the alleyways and I can't help you," she said pointing to Twilights flank. "I don't have the magic of friendship anymore Twi."

"Wait what the magic of, bwahahahaha that is probably the..." he looked around they weren't joking, "most creative thing I have ever heard."

"I can't fight but I can get you in udetected," she said. Twilight hugged her.

"I knew you still had some loyalty in you, now we need to get into that castle."

It was hours before they left. They twisted in and out of alleyways. Past crumbling buildings and destroyed statues. As they approached the castle Rainbow stopped.

"This is as far as I go," she said. While they were looking for the entrance Rainbow was talking about, Rainbow grabbed her tazer and magic suppressor. She zapped the Doctor and Derpy. And slid the suppressor over Twilight's horn. Twilight turned around just in time to see a hoof and then everything went black.

Chapter 5: The Possible Defeat

Twilight had been hangig there for hours it seemed waiting for Tirek to finally just get it over with. But for some reason Tirek wasn't even here. She looked at her surroundings she was in the throne room. The windows were shattered and the roof had partially caved in. Then there were large hoof steps and Tirek walked in with three changlings.

"Have you found that blue box yet," he sounded angry.

"No sir," one said he had been given the job of telling him news. The next thing he knew he was flying out a window.

"Its a blue box how can you not find it," he yelled sitting down in the throne.

"It seems to just have disappeared sir," another said.

"Things don't disappear they fade out and then fade in somewhere else," Tirek yelled.

"You'll never get the Doctor," Twilight laughed. This wasn't the best time to do this as she said it Tirek got off his throne and walked over to her.

"So you know how to find him," he said with a smirk on his face.

"Yes but I won't tell you," she said. Tirek laughe.

"Fine then maybe we can trade," he said pointing at her friends.

"Not this time Tirek," she said looking away from Tirek. This made Tirek quite angry.

"What do you want then," he yelled. He slammed his fist into a wall and the wall nearly shattered like glass.

"I want you to go back to Tartarus as weak as you came," she said," and return everypony's magic to them." The TARDIS was suddenly there and out ran the Doctor.

"Don't do that he killed almost every one of your friends in the dungeon," he said pointing behind him. There stood the weak Rainbow Dash her fur a very pale cyan and her mane was everywhere. She looked over at her with a saddened smile. This ticked Twilight off. The suppressor snapped at the sudden surge of magic and the blast smacked Tirek in the back of the head.

"Why you little pest," he said opening his mouth to drain her magic. Twilight teleported away in time and started towards the TARDIS. Tirek was above her in seconds. She teleported the rest of the way and she closed the TARDIS door. She looked over at the Doctor and noticed he was already hitting buttons and pulling levers.

He got a call picked up the phone and yelled, "not right now," and hung up. He pulled one last lever and the were soon gone from the throne room. They're bodies started to change as they went from pony to human.

"Doctor why are we headed to another dimension," she said. She looked over at Rainbow. She was looking at her self as she transformed. Twilight quickly realized that Rainbow would need clothes soon and ran to where she left the clothes Doctor had packed for 2 people. Just in case that was the case. She tossed them to Rainbow who gave her a questioning look.

"I suggest you put them on," the Doctor said,  "you probably would prefer to so you don't um become curious about your body."

"Why would I do that," Rainbow asked trying to understand where everything went.

"Let me help you," Twilight said. She grabbed Rainbow by the arm and pulled her down stairs. The Doctor turned to Derpy who had already gotten human clothes on. Then he called a dimensional store.

"Hello," said a british man," how may I help you."

"This is The Doctor I am requesting under the name of another dimension that we get a magical transfuser and about 30 tons of steel rope." The phone went silent and then there was a loud bang.

"Anything else," the man said. And some fish and custard please. Also some salad. No dressing," he said like he was placing an order.

"Please open your dimensional port and the objects you have ordered will be there soon," he said and hung up.

"So wait why should I be wearing these," asked Rainbow walking up the stairs with Twilight. Rainbow had a t-shirt on and jeans the t-shirt was white and she looked like she was very uncomfortable with what lied underneath her clothes. "Don't worry you'll get used to it," she said.

"Its kind of a rule in a lot of dimensions," Twilight said pointing at her clothes," they keep private spots from being seen in public."

"Exactly, and where we are headed there won't be people for miles but that doesn't mean we don't need them," he lifted up his dimensional transport port and sure enough two bowls one with salad and the other with fish and custard were inside. He handed the bowl to Twilight.

"I'm sure she is quite hungry," he said pointing to Rainbow. She had gotten interested with a little tool. "No stop that is my Sonic Screwdriver," he yelled he ran over and tried to pull it out of Rainbow's hands.

"Nope sorry," she said moving out of the way. He fell down a flight of the side stairs.

"That is not a toy," he said dazed. He started up the stairs with a run only to be stopped by a bang as 30 tons of steel rope hit the ground. And fell onto the stairs. "Crap," he said as he was soon swallowed by the rope.

"Hehehehe," Rainbow laughed and started messing with the screwdriver. She pointed it at the door of the TARDIS and clicked the button. A click was heard. The door was locked.

"Stop," he yelled. She was soon locking anything with a lock visible. The Doctor quickly ran up and grabbed the screwdriver.

"Hey I wanted do something cool," she said crossing her arms.

"Well do it somewhere else with something that isn't my Sonic Screwdriver," he said stuffing it in his pocket.

"Now you are probably wondering why i'm taking us to another dimension," he said going to his transport port again. He pulled out a large box. It had light and levers everywhere. There were two deflated sacks on each side.

"Why," Rainbow asked eating the salad that Twilight had handed to her.

"Because after I increaed the reach of the TARDIS so that Tirek came along for the ride I neede to find a dimension where he would become human as well. He will be strong though so that is why I have the rope."

There was a sudden knock on the door they all knew there was only one person who could be out there. The knocking became more and more persistent and there was a crack. The door snapped and outside stood a well built man had a horse body.

"Wait you said he would be human," Twilight said.

"Yes I did but he would still be a centaur. Just smaller," he said and he quickly tossed the rope to Derly and Rainbow. "When I give the signal," he said he pulled out his sonic screwdriver and opened a back hatch. He ran out with Twilight and they started to find ways to get Tirek to become weak and vulnerable. The fight was about to take a turn no one expected

Chapter 6: Well now what

"We are getting nowhere with Tirek," Doctor said getting Tirek to slam into a mountain side," we've been at this for hours."

"Actually only a couple minutes," Twilight said. They were in a wide plain with the occasional tree. To their left was a large mountain cliff. They had been trying to get Tirek to charge fast enough he'd smack his head a little to hard.

"Well it feels like it, i'm sweating over here," he said wiping his forehead.

"You have a trench coat on that is why," Twilight yelled. They were switching back and forth between who had Tirek chase who. Tirek charged at Twilight and she moved away in time to see him smack his head into a tree. This time Tirek showed the slightest dizziness.

"We're getting to him," Doctor yelled. Tirek quickly returned to an unaltered state. This time he stood there and Doctor knew what that mean't he had gotten wise to their tactic.

"And here I thought you were going keep fighting like chickens," Tirek said.

"I am not a chicken, i'm a time lord," Doctor said. Tirek started walking towards the Doctor.

"I know who you are Doctor," Tirek said.

"Really then do tell me what you think," he said. He smiled and went into his coat pocket. He pulled out his sonic screwdriver and pointed it in the direction of the closest tree. "About a tree exploding in your no longer immortal face," he smiled.

"You're bluffing," Tirek laughed.

"Try me," the doctor twitched his hand and Derpy and Rainbow dropped from above the mountain onto Tirek. They brought down the ropes with it and tied him to the tree.

"And now what do you plan to do,"  Tirek asked.

"Well first of all I was bluffing but now I have something I can use," he pointed the sonic screwdriver at the metal. "To many sound waves bouncing at you at a high enough frequency can shatter your bones," Doctor said.

"Twilight help us move this," Rainbow yelled they were having trouble moving the transfuser. The magical transfuser was soon right next to Tirek and all they had to do was hook it up and get the magic out of him. Then a large shadow fell upon the four. In the sky was a large saucer shaped ship. It was armed with lasers on every rotation.

"Well shoot," Doctor said.

"The Doctor has been found and he will be exterminated," a large, unemotional, sounding voice yelled. Doctor knew that voice all to well.

"Everyone get to the TARDIS," he yelled. This gave Tirek the distraction he needed to break the rope. "Well it turns out I must have needed stronger rope," he said looking back.

"What are we running from that's in that ship," yelled Rainbow.

"Daleks, they're a very old enemy of mine," he said," they locked my home planet in a pocket dimension." Rainbow just gave questioning look.

"Ok what do Daleks even look like," Rainbow asked. Just as she asked Daleks teleported in front of the TARDIS.

"Doctor Who has been located engage extermination," a yellow Dalek said.

"Hold on a new creature approaches," said a blue one. This strange creature was Tirek and he was charging right at them.

"Ignore the Doctor a new much bigger threat approaches," said an orange. Tirek was gathering ground quickly and his head lowered just in time for him to strike a Dalek smashing its top half to pieces. The other two started blasting Tirek and all they did was leave scorch marks. Tirek turned around towards the TARDIS and just began walking towards it.

"Retreat," said the yellow. They were soon teleported to the mother ship and they began to open fire on Tirek. With once again no change in the centaur's movement.

"Wait, nows our chance," Doctor said. He activated his screen communicator and a Dalek appeared. It was white and spoke in a much deeper voice than the rest.

"Doctor what is this thing," yelled Dalek Prime.

"His name is Tirek and he is, on the human planet, called a centaur. He right now holds quite the immense amount of magic," Doctor said.

"How do we stop it," Dalek Prime asked.

"The only way I can stop him is if you get him to stay in one spot," he began," and then I can suck the magic out and you can defeat him."

"We can use the forcefield and you can begin to take his magic away," said Dalek Prime.

"Good now if you hold him lon enough that should be possible," so he grabbed his sonic screwdrver and ran out to get the transfuser.

"Soon the Doctor will die," said Dalek Prime as he turned towards the other Daleks," and we will finally exterminate the entire galaxy of anything not created by the Daleks." The Dalek turned back towards the viewing panel and saw the Doctor running with the transfuser. They raised the forcefield around Tirek and watched as Doctor started the magical transfusing process.

"Now this might hurt a lot but don't worry you won't die," Doctor said as he activated the transfuser with his sonic screwdriver. Tirek screamed in pain as the magic was sucked out the same way it went in. Doctor quickly amplified how much magic the entire thing would take at a time. And the magic poured out of Tireks mouth like a waterfall. As the transfuser became full the last drop of magic left Tirek's mouth. He was now a small centaur compared to his original size. Then the Doctor was instantly on board the Dalek spacecraft. All around him were Daleks lasers pointed right at him.

Chapter 7: This isn't the End

Rainbow watched as The Doctor disappeared instantly. The forcefield around Tirek lifted and also disappeared.

"Where did he go," Rainbow asked. She needed to know.

"The Daleks took him onto their ship," said Twilight. She then pointed to the flying saucer above.

"Well what do we do," Rainbow asked.

"We get the tranfuser in the TARDIS and we wait," Twilight said," he'll find a way off." She looked over at the TARDIS. Derpy had already begun opening the door. They grabbed the transfuser and headed towards the TARDIS.

The Doctor was surrounded by Daleks. They were in the Dalek command station. The panels to pilot the ship and for the lasers were in a large circle. Each panel had six domes one to do a different task.

"What gives I just helped you guys not become scraps," The Doctor said.

"You were only of one use," Dalek Prime said," the path to your destruction. Prepare to be exterminated." He had to think fast or he would have quite the problem on his hands.

"Hold on now, can't you at least let me do one last thing," Doctor asked.

"No," Dalek Prime said. They all prepared their lasers for the destruction of the Doctor. When he pulled his sonic screwdriver out and pointed at the nearest control panel. The whole ship lurched forward and the Daleks started rolling around. Firing but missing they all tried to get the Doctor. But he had already caused to much interference with the controls. The ship was moving around in random directions.

"What was that about not getting to do one last thing," Doctor laughed," now if you'll excuse me." He pointed his sonic screwdriver at another control panel and he was sent back down to the planet below.

Doctor entered the TARDIS to find them all waiting patiently.

"Well you guys seem to be awfully calm," Doctor said.

"Doctor, oh am I glad to see you," Derpy said. She ran over to him and hugged him.

"By the looks of it you knew I would be back," Doctor said chuckling. While he was gone they had put the door back on the TARDIS and repaired it as much as possible.

"Now where to," Rainbow asked. She knew where but she didn't want to go there.

"Equestria," Doctor said," to give this magic back to the people of your species." He started flipping switches and pulling levers and pressing buttons. The TARDIS then made the familiar whirring noise and they were headed back to Equestria.

As they left the TARDIS they got quite the surprise. They had returned to the throne room and on the throne sat an alicorn. Her mane not flowing. Her fur was a dirty white as if she had been rolling in dirt. She was smiling though as if she knew they had defeated Tirek. The Doctor bowed and said,

"Good afternoon your highness," he said. Twilight galloped to Celestia and nuzzled up against her. Celestia embraced this with a hug.

"Thank you," Celestia said," all of you. I wish I could have helped but sadly I couldn't."

"There is no problem I do this all the time," The Doctor replied. Celestia just looked at him with a confused look.

"I don't remember you," Celestia said.

"The name is The Doctor," he began," I travel through time and space with the blue box behind me. I am from another dimension. I like to keep myself a secret though so don't tell anypony about me." Celestia nodded and turned to Rainbow and Twilight.

"I want to know how you're going to get the magic back to evrypony," Celestia asked.

"I can answer that one," Doctor who said," shots. The kind that you give to sick ponies and stuff like that."

"And what if they don't prefer that," she asked.

"It would take me a while but," the Doctor said," I could also hook it up to a large dispenser and we could spray it all over Equestria."

The air felt magical. Thats because it was the dispenser had sprayed all the magic over Equestria.

"Hey Doctor," Twilight said. "What do you plan to do now." The Doctor was reparing the door of the TARDIS to its full restoration.

"Well I hear they're celebrating this tonight so i'll stay for the next few days to help clean up," he said pointing to the rubble everywhere.

"Then what," she asked.

"Go off to help another person and their problems," he said as he used his sonic screwdriver to screw in a screw.

"Ok well hope you have fun," Twilight said. She trotted off to watch the pegasi fly after almost 2 years.

The air was warm and the atmosphere was happy. The party had only started ten minutes ago and everyone was already congratulating Twilight for her defeating Tirek. Doctor sat at a table looking into a glass of punch.

"Hey Doc," Rainbow yelled,"come on Doc join the party." She trotted over and sat across from him.

"No thank you Rainbow Dash," he said still staring at the glass of punch.

"What's wrong Doc," she asked.

"Nothings wrong its just that i'll be traveling the universe alone again," he said looking up from his punch. He hated traveling alone he just really didn't like being alone at all.

"Come on Doc," Rainbow said," you have Twilight or Derpy. You wont be alone."

"No Rainbow I will be alone," he said," I wont be taking them along."

"How come," Rainbow asked.

"Because they're just to," he said," you know."

"Yeah I guess you're right," she said. Then she started thinking about asking him if she could come along. Then she heard it a very familiar voice.

"Congratulations Twilight," Discord said grasping her hoof with his claws," finally you came back to save Equestria."

"Thank you Discord," she started," but I couldn't have done it without Derpy and Rainbow.

"Rainbow Dash is still alive," he looked around searching for her. She spotted her and The Doctor and teleported over to them.

"Who's he," Doctor asked.

"Discord that's who," she said. Discord appeared next to Rainbow.

"Thank goodness somepony else other than Twilight and Fluttershy is alive," he said hugging her," it was so hard thinking we would never see you again."

"That's nice Discord," she said," but you should just go talk with Twilight some more."

"You're right there are so many questions," he said as he teleported to Twilight.

"Hey Doc do you mind if I come along with you on your adventures," she said," I really have nothing to look forward to."

"I'll think about it," he said. The rest of the night consisted of them talking and sharing their own adventures. Laughing and chuckling at their stories. As the party died and everyone went home the Doctor said,

"You can come along with me."

"Yes, sounds awesome," she said doing a loop.

"But you have to listen to me," he said," whether it be I want my sonic screwdriver, or something else." He knew she would still do the occasional ,not going to give it back thing, but he thought that was the best thing about her.

"Fine," she said grinning. They trotted off towards the castle and worked on the clean up with the rest of the ponies who had volunteered.

Chapter 8: The Clean Up: Part One

The halls of the castles were just destroyed in every sense of the word. The cleaning was quite the hard job as there weren't many who wanted to help clean. The ones who did were either guards or Wonderbolts. The Doctor was one of the stallions who had to take the cart of destroyed plaster and wood to a pile outside the castle. Rainbow and any pegasi were removing broken glass and wall that couldn't be reached. Twilight was moving piles of trash from the ground to the carts along with any unicorns.

"So," Doctor said as he approached back with an empty cart," what do you plan to do when this is over." Twilight looked at him and shrugged her shoulders as she dropped trash into his cart. Then Doctor started in the other direction.

"Hey Twilight," Rainbow yelled," we got a fresh pile of broken glass over here." Even though Twilight didn't like the fact that the unicorns had to put trash in the carts, she knew that if she stopped she might disappoint Celestia. So she used her magic and waited for a stallion to walk up with a cart.

The Doctor had just dropped a pile of trash when he noticed a glimmering object in a nearby pile.

"Now isn't that strange," The Doctor said as he got closer," I don't think this should be here." He pulled the object out to see just a scrap of gold from a statue. He just chuckled and dropped it. He just thought it would have been something more interesting. He flipped it over hoping to find something. He didn't it was just a piece of gold. He didn't know why but, this gold just seemed out of place. He picked it up and tossed it in his saddlebag. Then he turned around and headed back towards the castle.

The hall they were in was almost done. They had just cleared out the rest of the broken pillars and smashed wall pieces. They were just waiting for the last stallions to take the trash down.

"So Twilight," Rainbow said," do you want to hear what happened after you left?"

"Maybe later," Twilight responded. She did want to know but not right now. There was so much to do.

"Ok, whatever you say," Rainbow said. Thentoo stallions approached and and Twilight dropped the trash into their carts.

"We'll be moving onto the next area so please meet us there once your done," Twilight said. The stallions nodded and trotted off.

The next area was the dining hall and oh boy was it messy. The tables were smashed and everywhere. Half the place had collapsed and the doors were nowhere to be found. Dust was everywhere and the occasional rotten fruit or vegetable. To think years ago this place was meant to be used to celebrate occasions. Today was its first day in a long time to be used or walked in by the looks of it. The first thing they did was plan out what to get rid of first. Of course the rotten food was to be tossed out for decomposition. The next thing would be the ceiling. They started shifting through the wreckage for anything important.

"Hey I think I found something," yelled a guard pony. They all moved over to him to find a note in the wreckage. It read

Dear Celestia,

I know that i'm just your regular guard but, I have found some interest in you. If you are reading this and i'm not there then Tirek or the changelings have gotten me. I love you Celestia.

Sincerely,

Paradox

Twilight picked up the note and folded it. She turned towards a guard pony. "Take this to Celestia please we don't want to throw this out. In memory of this Paradox pony."

"Yes Princess Twilight," he said. He picked the note up and galloped off to find Celestia. Then they continued to search through the wreckage. What they found next they wish they had never seen. A mangled body laid there. Its head snapped and its eyes wide. It had no cutie mark. It was a stallion with a red mane, they hoped that it was naturally red. His eyes were green with a bright tint to them. His horn was snapped and his body was a grayish color. The body was cut in several places. They all hung their heads in sorrow. Twilight suddenly made the connection. This was Paradox he had been crushed surviving in the shadows and destruction of the castle.

"Rainbow, I hate to ask this but could you and one of the wonderbolts carry this body away," Twilight said turning to Rainbow.

"Yeah, of course we will," Rainbow replied. Her and Spitfire grabbed a set of hooves and flew slowly out the door. They were going to bury it but not right now. Twilight and the rest got back to work picking through the rubble. They finished their search and started cleaning the room. The stallions returned along with The Doctor and they started loading trash into their carts. As night approached they stopped and headed towards their living quarters, or in the Doctors case the TARDIS, and went to bed.

The Doctor was still awake he had been trying everything he could to find out why this piece of gold had seemed so important. He had found out it wasn't gold but a piece of something else. Copper which was usually found in statues. But the hall they had been in didn't have copper statues at all. So he was still confused as to what it was. He gave up and went and laid down. He would ask around tomorrow about it.

Chapter 9: The Clean Up: Part Two

The Doctor was up and getting ready for day two of clean up when there came a knocking at the TARDIS door. He walked over to the door and opened it a bit. Outside there stood Rainbow with a tray. He opened the door wide enough to let her in.

"Hello Rainbow what's that," he said pointing to the tray.

"Breakfast, duh," she said as she set it down on the Doctor had been using to study the copper piece. The tray consisted of apple pancakes and a sliced orange with a glass of water. He walked over and sniffed the apple pancakes.

"Ugh," he said scrunching his muzzle," what is that?"

"An apple pancake," she said giving him a quizzical look," why?"

"Nope I hate apples in any form won't eat them, won't even touch them," he said shoving the tray over.

"Come on Doc you gotta eat," Rainbow said moving the tray back over to him.

"I'll have the orange and the water nothing else," he said grabbing an orange slice with his mouth and started chewing.

"Suit yourself," Rainbow said as she picked up the pancake with her mouth and dropped it on the Doctor's head.

"Hey," he yelled as he got off his haunches. He turned towards Rainbow and started after her. The Doctor chased Rainbow for a while before tiring out. They both sat down and waited until they caught their breath before speaking

"Ha ha ha. I'm really going to enjoy your company," the Doctor laughed.

"I'm sure you would have no matter what," she said as she started towards the door," oh and by the ways, clean up started." She walked out the door and headed towards the dining hall.

Twilight had just finished sorting through some rubble piles they had made the night before when the first stallions came with the carts. Twilight loaded their carts and sent them off to get rid of the rubble. Rainbow then approached with the wonderbolts to deal with the ceiling shards that were to dangerous to keep connected in fear of them falling. As Twilight started making more piles the Doctor arrived with his cart in tow.

"Um hey Twilight," he started as he dug through his saddle bag," can you tell me if there was anything copper related in the halls we had cleaned up."

"Not when we started cleaning no," she said," but when I was running through the halls I saw the occasional statue made of copper." She had remembered these statues because they memorialized Queen Chrysalis in the most taunting poses ever. This copper obviously meant it fell off a statue. Which meant that the changlings had probably packed the statues when they left the castle and kingdom all together to fast to realize the broken piece on a statue.

"Oh well then I guess it was pointless staying up all night trying to find out why it was here," the Doctor said. Twilight loaded his cart laughing. She then loaded the cart and sent him off. The rest of the clean up was the same routine. Stallions came back and forth. While Twilight dropped the rubble into their carts. By lunch they had cleared out all of the broken ceiling. The tables would be rebuilt and refined to take more weight. They decided they had earned a lunch break and went to get something to eat.

Canterlot was in a better shape thanks to the hard working ponies outside the castle. Some restaurants were already opened and running again. Houses had either both floors or a floor and a half. Trees had been replanted and gardens were being worked on. The Doctor decided to stop at a restaurant by the name of Soul Foods. Inside was quiet, just the way he liked it. With the occasional clanging of glass against silverware. He approached the front counter to see a young foal with a red mane and yellow fur. Her eyes were orange, but she had bags under her eyes. It was Applebloom. She had obviously taken the job to help with the ponies in Canterlot to help with the destruction and lack of workers. He felt a little sorry for her she didn't look like she even wanted to be here.

"Hello sir what can I do for ya," Applebloom asked.

"Hmmm," he looked at the menu and noticed a familiar word, Fries. At least they still had some food from the human world that wasn't fruit or vegetables.

"I'll have some fries," he said.

"Alrighty," she turned around and yelled back to the back," we got an order of hay fries!" The Doctor turned around and went and sat at a table. He looked around to get a look at the ponies around him. Some were old and reminded him of someone he couldn't put his finger on it. Another looked strangely familiar like he was supposed to be a copy of someone who he wanted to save at one point.

"Here ya go sir," Applebloom said placing a plate of hay fries in front of him.

"Thank you," he said as he placed a few bits on the table. Applebloom picked them up and walked away. He picked a hay fry up with his mouth and ate it. It tasted almost exactly like regular fries. A few minutes later he left and started back towards the castle. He still couldn't tell why that one pony looked familiar. Well it might become clear to him sometime after he leaves Equestria.

With the clean up just finished in the dining hall they moved on to the next hall. It wasn't as damaged so it wouldn't take long. It only had a few broken pillars and windows. They started working as this would be the easiest hall yet. The cleaning only was worth three carts so they moved on. The next area was the grand hall and it was a mess. The windows were completely shattered. The glass was everywhere and pillar remnants were scattered all over. There was the occasional guard armor. That could've meant that the whole grand hall was a battle ground at one point. The railings were broken in places and there were chunks in the stairs missing. The doors were destroyed and shrapnel was everywhere. This was going to be a long job and there wouldn't be much time to relax tomorrow.

"Well this is gonna be a long clean up," Rainbow said.

"Yes, but we will get it cleaned," Twilight said," so lets get started." They all started by picking up the door shrapnel and placing it in a large crate the pegasi had brought from the storage room of the castle. With the door shrapnel cleaned the next was the actual destruction. The stallions brought the carts to the front of the castle and waited for the rubble to be dropped into the carts. By the time night fell they had only cleaned only a quarter of the destruction. They all once again returned to their living quarters.

The Doctor just couldn't sleep with the feeling of knowing that pony from somewhere. He looked so familiar and yet couldn't remember who he was. So he decided to go have a little talk with an old friend. He activated the TARDIS and was soon gone.

Chapter 10: The Final Day: Part One

Rainbow was sitting at a table. This table was right in the hall the TARDIS used to be. she had come down to check on The Doctor when she saw it was gone. She was tapping her hooves together when Twilight approached. Twilight was using magic to hold a piece of paper.

"Hello Rainbow," Twilight said," Fluttershy sent us a letter saying, she wishes she could be here right now but she has become ill and won't be here for a few days." About then Twilight noticed the uneasiness that Rainbow had been feeling. Rainbow's mane was even more roughed up than usual. Her eyes didn't show any signs of sleep deprivation, so that means either she had a rough night or she had been rubbing her head to much. She looked worried and yet it was pretty hard for an average pony to tell, she had just become still when Twilight approached.

"Yeah, ok," Rainbow said, " tell her I hope she can make it when the clean up is done." Twilight expected Rainbow to be a bit excited that Fluttershy was still alive and sort of well. Twilight rolled the letter up and looked a bit more at Rainbow and how she was feeling. Only two days ago Rainbow was still in a jail cell and Twilight feared Rainbow might start suffering from depression or still is. Rainbow just began tapping her hooves together again.

"Rainbow are you okay," Twilight asked.

"Yeah Twilight i'm fine," Rainbow replied, once again she stopped tapping her hooves.

"Are you sure," Twilight persisted," I can do a spell that could probably help with your problem."

"Twilight i'm fine don't worry," Rainbow said with an annoyed tone. Rainbow hated when Twilight got to worried about her friends and their conditions even if it were just a small nose bleed.

"Okay Rainbow but if you need anything," Twilight started," I can..."

"I said i'm fine Twilight," Rainbow was even more annoyed now. Rainbow got up and started down the hall. That's when Twilight noticed the TARDIS wasn't there.

"Hey Rainbow," Twilight said catching up to Rainbow," where's The Doctor?"

"I don't know Twilight," Rainbow said. Twilight wasn't sure but it looked like Rainbow lowered her head a bit.

"Well I know he'll be back later," Twilight said," he always does come back." They went towards the grand hall to start the rest of the clean up. It was only four in the morning but they knew if they started early they could finish by late in the afternoon. As they entered the grand hall they stopped in their tracks. There sitting at the middle of the room sipping some tea was Discord.

"Discord," Twilight yelled. She looked around to find everything cleaned and in front of the stairs was a blue box with a stallion leaning against it.

"Oh hello Twilight," Discord said as he teleported next to Twilight," do you like the job I did. Wonderful isn't it." He spread his arms out as if to show them everything all at once.

"Discord, I thought you were taking care of Fluttershy?" Twilight asked.

"Oh I was until I brought her along," Discord began," she's in town and very well. When did you get that letter?"

"Well it was delivered two days ago but she said she had gotten sick and won't be around for a few days," Twilight said.

"Oh well the doctor we went to was wrong and she was sick for a day," Discord said. He was now back in his sear drinking tea. The Doctor then approached the two.

"Hey Rainbow," he nodded his head at Rainbow. Rainbow nodded back. "Hello Twilight," he said turning to Twilight.

"Hello Doctor," Twilight said," so where did you go."

"Oh that's none of your business," I just went to talk to an old friend."

"Who was this old friend," Twilight asked.

"That also is none of your business," he said," the thing that matters is that i'm back." He looked at Rainbow and Twilight hoping to see an agreeing nod. What he got was an angry glance instead.

"Well then I guess you wouldn't care if I asked where you were," Twilight asked," would you?"

"I was in Great Britain," he said," I won't tell you where in Great Britain but I was there." He was slowly being advanced upon by Twilight and he was slowly trying to keep the distance between him and her. Rainbow just sat and watched. She was as confused as ever.

"Male or female," Twilight asked picking up the pace.

"Male," Doctor answered," why do you care?" Twilight had backed him into a wall he was waiting for her to hit him with something. Instead she patted him on the head and kissed his cheek.

"Good," she said turning around," as long as it wasn't another mare." Doctor relieved himself and regained his composure.

"Then why did you keep advancing on me," he asked.

"Because otherwise you probably wouldn't have told the truth," Twilight said. She smiled a bit and then turned towards Rainbow and walked out the door. Discord was gone which means he had either gone to talk to Celestia or headed into town to talk to Fluttershy. Rainbow walked over to Doctor and gave him a hit on his shoulder.

"Ow what was that for," Doctor asked.

"You left without telling me I was afraid you had left and weren't coming back," Rainbow said.

"Well I came back didn't I," he said. Rainbow hit him on the shoulder again.

"Well you didn't tell me I was afraid Doctor," she said.

"Okay i'm sorry I left without telling you," Doctor said hoping this time for a hug. Instead once again there was a strike to his shoulder.

"And," Rainbow asked.

"And I didn't even leave a note and almost gave you a heart ache," Doctor said. Rainbow jumped back a bit.

"I don't love you," Rainbow said. Doctor just rolled his eyes as if to say, yeah right. This got him another strike to the shoulder.

"Stop that," he said.

"Well then don't give me that look again," she said. Doctor just stood there not moving. "I want to see you agree to that."

"Fine, I The Doctor here by say I won't, ever, give the mare, Rainbow Dash, a roll of my eyes," he said in a court room voice. He once again was struck in the arm.

"I'm serious," she said.

"I know I was joking seriously," he said. Rainbow just looked at him sternly. "Well want to go say good bye to all your friends and family," he started," this is going to be your last day in Equestria for a long time."

"Not yet I need to go to all my friend's funerals," she said. At that point she saw herself eating what was left of Applejack. She had done it because she was starving. They all had been starving and they all started attacking each other. Taking bites out of each other when they could. Applejack was the last one to go. She had grown smart to everyone's tricks. But that was her downfall. By keeping herself safe she starved herself to the point of lunging out at Rainbow. She had died by striking her skull against the wall repeatedly. The last words she said once again echoed in Rainbow's head.

"Make it stop," Applejack had said," just make it all stop." Then there was the crack and Applejack had gone limp.

"Rainbow, Rainbow Dash are you there," the Doctor asked waving a hoof in front of Rainbow's eyes. Rainbow shook her head and looked at the Doctor. "So are you gonna tell me what you were thinking," Doctor asked.

"Maybe later Doctor," Rainbow said. She started towards the door. She was almost out when there came a breeze and up above came Celestia carrying a saddlebag. As she landed she greated Rainbow and The Doctor.

"Hello Rainbow," Celestia said. Her voice was so clear and soothing. She had a kind expression on her face. Celestia went into her sadllebag and retrieved a rolled up paper. She unrolled the paper with her magic and turned it towards Rainbow for her to read. The letter said:

Rainbow Dash,

Today at 7:00 p.m. will be the funeral of the following: Rarity, Pinkamena Diane Pie,and Applejack. If you have the time please stop by. We hope to see you there. And we are very sorry for the loss of such great friends

Rainbow Dash had cringed at the last name. She didn't think that she would be the one standing over Applejacks grave. She thought it would be Twilight being the one standing above everyone's grave.

"So Rainbow we're going to be there, right," Doctor asked.

"Yeah, I guess," Rainbow answered.

"Hold on Celestia why are you the messenger pony," Doctor asked turning towards Celestia.

"The usual mail pony is helping get Cloudsdale up and running again," She said. She pointed towards Cloudsdale and Doctor got a look at pieces of clouds being moved back into place. Celestia then took off and headed in what looked like the direction of Fluttershy's cottage.

"So what do you want to do until seven," Doctor asked.

"I don't know," Rainbow replied.

"How bout we walk around and see what we can find instead," Doctor said.

"Why not we have a lot of time to spare," Rainbow said. They started off towards the town and were soon among the crowd of ponies.

Chapter Eleven: The Final Day: Part 2

The castle was very quiet that afternoon. The only noise was of the occasional cough. Rainbow, Twilight, Fluttershy, Derpy, and Doctor were standing around in the TARDIS. Fluttershy had entered earlier and was now sitting in a chair looking at everything. The TARDIS lights were dimmer than usual because the Doctor had thought it appropriate due to the event happening in an hour.

"So this place what is it called," Fluttershy asked.

"The Time and Relevant Dimensions in Space," the Doctor answered," also known as the TARDIS."

"Oh well it looks.." Fluttershy began.

"Small on the outside yes," Doctor said," but there is more to this place than just what you see."

"Doctor since you and I weren't invited to the funeral you want to go and have some fun," Derpy asked.

"Actually, Rainbow wanted me there but," he said as he looked at Rainbow," she has her friends to be there for moral support."

"Yeah what did happen down there Rainbow," Twilight asked. They all looked at Rainbow and waited.

"Well," she started. The images entered her head again. She started to tell the story.

"Let me go you monsters," Rarity yelled. Her mane was a mess, her fur dirty, and she had a magic suppressor on. She was trying to get at the changelings who had her restrained. The changlings weren't even the slightest annoyed at the insults she had been throwing at them for the past few minutes.

"Common Rarity it's pointless," Applejack said. Her mane wasn't any better. She had a little changling blood on her hoofs. Her and Rainbow had tried their best before being overwhelmed by changlings.

"Okay so now what do we do," Pinkie asked. She had the second most restraints on her. One on her tail another on her waist and neck. It was all to keep her still.

"Nothing Pinkie," Rainbow said," we lost." Rainbow had restraints everywhere. On her wings, her hooves, her knees, and her neck. They approached the cell and a changling opened up the door. They were soon all on the ground in the middle of the cell. Rainbow quickly got up and ran to the door. The door closed just in time for Rainbow to hit her head. The world spun for a few seconds and she dropped to her haunches.

"Uh those big meanies," Pinkie said. They ran to Rainbow who was rubbing her head.

"Rainbow you alright," Applejack asked.

"Yeah my head just hurts a bit," Rainbow said getting up.

"What do we do now," Pinkie asked.

"Ah guess we wait. Twilight should be here fer us eventually," Applejack said.

"Yeah when she gets back with that handsome stallion," Rarity said. They all sat down in corners occupying themselves and started waiting for food. They soon all fell asleep and the next thing they knew there was a knocking at the cell door.

"Get up," yelled a voice. It was a changling he had brought them what looked like a small celery stalk. It was rotten and molded. He dropped it through the bars. Pinkie looked at everyone else and so did Rainbow. They were hungry but they weren't that hungry. The changling walked away and everyone started talking.

"So that's what we're having for breakfast," Rarity said. She was sitting in a corner of the cell. Her mane had gotten even worse. The dirt on everyone had started to mat down their fur.

"Apparently," Applejack said. She walked over and picked it up. She threw it at the wall and it snapped.

"Wow, they really expected us to eat that," Rainbow said.

"I wouldn't have eaten it even if it were covered in frosting," Pinkie said.

"Ah think they're trying to starve us," Applejack said sitting down. She kicked a pebble across the cell.

"Well I guess they think we're lying about where Twilight is," Rainbow said.

"We can only hope that she returns in time," Rarity said," before we pass on."

"Don't say that," Pinkie yelled," she'll come back and save us before then."

"Well ah sure hope yer right Pinkie," Applejack said. The cell went silent and they all just laid down. A few minutes passed before Rainbow spoke.

"And what if she doesn't? What then," she got up and stomped her hoof on the floor.

"Then we'll hope that she comes back to save Equestria," Rarity said. Rainbow just sat back down. She could feel her wings getting stiff. There wasn't the room to fly or flap her wings. She hated it in there no room to do about anything. The rest of the day was filled with silence. As day broke, surprisingly, they all woke up one at a time. Rarity was the first to notice the sun rise.

"Wait why is the sun rising and setting," She asked.

"Well since Discord is still out there he probably took the job," Applejack said. She knew it was only for Fluttershy's sake but that didn't matter as long as there was a day and night cycle.

"At least it isn't changing every few minutes," Rainbow said. Then it hit her. She could use a brick to break the bars. She grabbed one and flew up to it. It hurt her wings but not to much. She struck the bar and a loud bang was heard. But it wasn't the bars that had made the noise. It was a changling who had struck the door's bars. A few minutes passed and the changling left. Rainbow began striking the bars again. Then the window was suddenly blocked and they heard a laugh. Rainbow threw the brick against the wall. The brick cracked and broke.

"Well that didn't work," Rarity said.

"Yah think," Applejack said.

"Well now there's like no light," Pinkie said. There wasn't much the rest of that day. Only a little fight over a few pieces of bread for lunch. The next day was the first day of any signs of someone cracking. Pinkie had started biting her hooves.

"Hey Pinkie are you ok," Rainbow asked.

"Yeah I just got the jitters," she said. She bit a little to hard the next bite and a little blood seeped from her hooves.

"Pinkie please stop before ya kill yerself," Applejack said. The next thing they knew Pinkie had jumped on Applejack and opened her mouth. Rainbow tackled Pinkie and smacked her.

"Pinkie snap out of it," She yelled. Pinkie's ears dropped and she closed her eyes. Tears started to form.

"I'm so sorry everypony," her hair deflated and she walked to a corner. The next thing was breakfast. The food was actually edible. A few apples and a bowl of water. Applejack grabbed the apples and handed them out. She smashed hers and took out the seeds. She went to a corner she had been beating her hooves at. There was a dirt patch and she dug up some dirt dropped the seed in and covered it again.

"How is that going to grow," Rarity asked.

"Ah know it will," Applejack said. She went to the bowl of water and dribbled some water onto it. Little did she know it wouldn't. The next fight had actually hurt someone it had started with another loaf of bread half covered in mold. A few punches were thrown before they realized the fact that they had crushed the bread in the fight. The next few days were filled with fights. The rations got worse and worse. With the exception of a few apples once and a while. The stench of unwashed pony filled the cell. Then it happened, the first death. Pinkie had quiet that morning she just laid there. Hour after hour she didn't speak or move.

"Pinkie are you okay," Rainbow trotted over and turned her over. What they saw was a bloody muzzle. Her legs had bite marks everywhere. Her hooves were cracked and they were seeping with blood.

"Oh mah god," Applejack yelled," what did she do ta herself."

"I don't know Applejack," Rarity said," but please turn the body back over." At that point she gagged and a little puke came up. Rainbow turned the dead Pinkie back over. Applejack yelled for a guard and one approached.

"Could ya please get that body," she pointed at Pinkie," out of the cell."

"Nope we can't trust you in sitting still while we carry it out," he walked away.

"Well that just sucks," Rainbow said. They all moved to one side of the cell.

"Well I hope she's in a better place," Rarity said. As days passed the rations worsened to the point of just an apple a week. They could tell the economy outside was getting worse as days passed. They knew because they could hear the occasional screaming of get back here or he stole this or she stole that. Soon it was Rarity's time to snap. She looked as calm as ever, but she was barely calm in her head. They had all began to starve. Pinkie's corpse was rotting. Rarity had started scratching the days into the wall. Rainbow had stopped even caring about what happened next. Applejack had started tapping the bars with her hooves. Rarity had gotten up and walked over to Rainbow. Rarity was almost above Rainbow when she pounced. Rainbow was slower than usual due to the fact she was in a cell. Rarity was on top of her in not time. She started snapping at Rainbow. Froth forming around the mouth. She had lost it and she was about to try and kill Rainbow Dash. Applejack smacked Rarity in the side of the head. There was a crack and Rarity's jaw went limp. That still didn't stop Rarity from persisting on taking a bite out of Rainbow. Applejack went for a hit again. This time the crack was loud and Rarity went limp. Rainbow got up breathing heavily.

"Well," Applejack said," guess it's just you and me Rainbow. Now if you snap before ah do then ah'm a tell you somethin right now. Ah'll know every trick you try."

"Applejack don't say that," Rainbow said," Twilight will be here before one of us snaps." She could tell Applejack was scared of that fact. Twilight woouldn't be back in time Applejack knew it. Time passed and then the fateful day came. The day Applejack lost it.

"So Rainbow," Applejack said pointing to the wall," how many days has it been, since we were in here."

"I don't know AJ," Rainbow said.

"Well ah think your about ta snap," Applejack said," I can tell." Applejacks ear twitched.

"Applejack," Rainbow started moving back," are you okay."

"Yeah Rainbow," Applejack said moving towards Rainbow," whydya ask."

"Um because you don't look like you are," Rainbow said. Her flank hit the wall. Applejack had backed her into a corner.

"Well Rainbow," she said," sadly ah'm a have to put ya down." Applejack lunged at Rainbow. Rainbow had her chance she turned and kicked at Applejack. She hit Applejack in the stomach and ran. She didn't get far before she felt a pull on her tail. She turned to see Applejack biting her tail.

"Common Applejack," Rainbow said," stay sane. For Twilight's sake." Applejack let go of Rainbow's tail. She sat there for a few seconds staring into space. Then it happened Applejack walked over to a wall. She started striking her head. Rainbow hadn't known but Applejack had started hearing voices. Not the voices that keep you sane. The voices that drove you insane.

"Make it stop," Applejack yelled," make it all stop." The cracking of her skull became louder and louder. Then one last crack was heard and Applejack became limp. From that day forward Rainbow started surviving off the dead bodies in the cell. The rations had stop coming completely. She was forced to feed off the flesh and meat of the three. She had gotten sick multiple times and had lost all hope. Then came the day the Doctor was thrown in the cell. She thought they were dead but wanted to make sure. So she tapped her hooves and waited. And then he spoke after seeing Rainbow. And Rainbow regained hope from months ago.

"Oh my god Rainbow," Twilight began," I'm so, so sorry." Twilight had tears in her eyes.

"Wow Rainbow," Derpy said," I hope that their ghosts don't come back to haunt you." Derpy shuddered at the thought. There was a knocking at the door.

"The funeral will start soon," said a female voice. She walked away and the ponies left the TARDIS.

"See you after the funeral Rainbow," the Doctor said. He and Derpy headed off in the opposite direction of the others. Rainbow, Twilight, and Fluttershy headed in the other direction. The funeral was going to be Rainbow's last memory in Equestria for a while.

Chapter 12: The Final Day: Part Three

The funeral took place outside near a newly made statue stand. On the statue stand it said.

In memory of

Applejack

Pinkamena Diane Pie

Rarity

Let them live on in the hearts of their friends and family

No one knew what would be put there as a statue. As Rainbow, Twilight, and Fluttershy sat down the priest of the Canterlot church began the cermenoy.

"Thank you all for coming. I'm sure some of you know why you're here. To mourn the death of Applejack, Rarity, and Pinkamena Diane Pie." As he spoke his weird moustache waved. He wore a robe and was a unicorn past his prime. "Now if we would like to have some words from the family and friends who volunteered to speak to those who didn't know about their dead family member." The first to go up was a red stallion. His blonde mane was pulled back. He had obviously used hair gel. Big Mac trotted up to the podium and began to speak.

"Applejack was always a good sister. She was hard working and kind," Big mac started," ah wish ah would've been there to tell her ah'll miss her. Ah want to thank Twilight for defeating the monster who ended her life." He looked out at the crowd and stepped down. He walked back to his seat. The next to approach was a lime green mare. She was old and slow. Her mane was in a bun. It was Granny Smith. She trotted up to the podium.

"Applejack was a great and wonderful granddaughter. She was so strong and athletic. She didn't deserve the death she got. Ah wish ah could've gone and saved her. But all ah can do is hope she is safer in the afterlife." Granny Smith got off the podium and trotted back to her seat. Now it was Rainbow's turn to say something about Applejack. She would be saying something about all three f them. She trotted up to the podium.

"Applejack was an awesome friend," Rainbow started," she was honest and kind. It is a pain to see her go. I know what it was like down there. She just like Rarity and Pinkie went insane in the end. She provided me with hope and I stuck with that hope. Thank you." She walked off the podium and back to her seat. The first coffin was lowered into its hole. They all knew what was inside, it is what's left of Applejack's body. As the coffin lowered Rainbow thought she saw Appljack near a tree at the edge of the cemetery. Then the coffin passed over and she was gone. Next was Pinkie's funeral. Mr. And Mrs. Cake weren't anywhere to be seen. None of the Pie family was there either. Rainbow was the only one to walk up to that podium. She looked across the rows of ponies watching and began. "Pinkie was an amazing friend," Rainbow said," she would always try to make you laugh and giggle. To bad her life came to an abrupt stop. I wish she had made it. To see this day of freedom." Rainbow finished and stepped down. With everyone done talking they lowered the coffin. Rainbow thought she heard Pinkie laugh and giggle. But the noise died as fast as it came. She thought she had seen Applejack and now she thought she had heard Pinkie. As the coffin was dropped and buried they continued the ceremony. Rarity's parents were the first to speak. Rarity's mother's voice was filled with heavy breathing. Rarity's father's voice was the same. They're speech was long and tough. With the occasional break to crying or pat the other on the back. Rarity's parents sat down and Sweetiebelle went up to the podium. Her squeaky voice wasn't as loud.

"Rarity was my only sister," Sweetiebelle began," she was my only sister and my favorite sister. I had hoped for her to be there for when I got my cutie mark. Sadly she won't be." She stopped to gather herself again. She was losing to emotions on a podium. "I wish I could have said goodbye before she died." Sweetiebelle ended her speech and went and sat down. Rainbow went up once again trembling.

"Rarity was a good friend of mine. She was always the drama queen of the group. But if she needed to she would get her hooves dirty. She had given us dresses for free before that day. I lost mine but I know some of us have their dress safe. Please don't lose them like we lost her." Rainbow once again sat back down. She expected to hear something Rarity had said. But instead nothing. She didn't see a Rarity or hear Rarity. The coffins were buried completely and the priest said final words to them all.

"We once again than you for coming. We hope that you get support with any bad feelings you may have felt. Please leave when you are ready." The priest trotted off. Everyone started to leave and the mingling died. Rainbow sat there thinking about why she had heard Pinkie and see Applejack. The cemetery was quiet. Rainbow trotted over to the burial place. She set down an apple seed. Right in the middle of the three. Then she trotted off. For the next few years this seed would become a tree. This tree will be the place Rainbow will come for comfort and when she feels terrible. This tree will be like those three to her.

"Alright so next stop Scootaloo's," the Doctor asked.

"Yeah just to drop off a letter," she said pulling a letter out of her packed stuff.

"Then on to have adventures," the Doctor pulled a lever and once again the TARDIS faded out of this area and reappeared in another. She stepped out of the TARDIS. They were outside a raggedy house. There was two mail boxes one for the raggedy house and another for the house next door. She flipped open the one on the left and put the letter inside. She trotted back to the TARDIS. They wouldn't be coming back for a long time.

Scootaloo opened the mail box. She took out the letter that was said to be for her. When she read the name she gasped. It was to her from Rainbow Dash. She opened it and started reading the letter.

To Scootaloo,

Hey Scootaloo, if you are reading this then I didn't get to see you before I left. I'm gone Scootaloo sorry. Wish I could have said this to you in person. Please tell Twilight to watch my house while i'm gone. And thank you Scootaloo for all those times we had fun. Have fun growing up and stay cool.

From Rainbow Dash

Scootaloo finished the letter and sat down. Behind the letter there was a feather. Rainbow's feather. Rainbow didn't want Scootaloo  to forget about her. But Rainbow had left. Where did she go? When did she leave? Will she be back? So many questions rolled through her head. She eventually got up and trotted of. She had to make sure Twilight knew about this.

She had fallen asleep in the TARDIS. She would obviously have been tired from all the stress and clean up. The Doctor dimmed the lights so she could sleep. He sat at a table thinking about that pony again. His beard had been short he had a moustache and his hair was a casual length. The stallion had been blonde or more of a white. It didn't matter that stallion had looked familiar. He just couldn't remember. Time passed and he got up and walked outside. It was a nice cool night on the planet they were on. He had landed on a hill. It over looked a town with children and parents walking around town. He sat down and looked at the town. He thought it was so peaceful. The children without a care in the world. The parents were just as oblivious. They would soon find out the truth below their town.

Rainbow dreamed a wonderful dream. A dream that she was back in Equestria with the others. They were having so much fun like from back in the day. She had never felt so happy in a dream ever. She just wished it were true. She wished they hadn't died. That they had lived through the pain. But sadly that wasn't the truth. They were dead and they weren't coming back. No matter how bad she wanted to see them again. Time was about to change for Rainbow. She'd be gone longer than she thought and the only thing anyone had to remember her by was a feather she gave to Scootaloo.

Chapter 4: The Truth

The Doctor woke up to the sound of cage bars slamming. He was in a jail cell about 30 bricks wide and no windows. The door looked like it was freshly cut steel. What light came in showed bones of a unicorn and two earthponies. He heard tapping and thought it was probably bones settling. He looked at Derpy who was still a little dazed. He knew that this Rainbow Dash character wasn't trust worthy but Twilight didn't listen. The tapping continued for quite some time and then he looked around a bit more in a corner sat a cyan pegasus.

"Wait what," he said. The cyan pony turned around to reveal itself as Rainbow Dash.

"So they didn't kill you," she said. Her body was thinned to bone on her hooves sat thin blotches of blood. Her mane was more red than any color, Her wing's feathers had started falling out.

"Wait if you're here then who is the other one," he said pondering and then he answered it faster than he asked it," changlings."

"Yeah," she said. Her face showed a hint of a you think face. "Tirek stuffed us," she pointed at the skeletons," down here and left us to rot until our friend Twilight Sparkle returned."

"Twilight Sparkle," he said trying to sound like he had no idea who she was,"  never heard of her." But then he remembered the day him and Twilight left.

"I know who you are," she said, "you're the Doctor who took Twilight with you." She looked angrily at him.

"I know I had just forgotten," he said, "now if you will excuse me I have a TARDIS to call." He rubbed his hair back to reveal a slot. In this slot sat a key. He hit a button on the key and the TARDIS formed around them.

"How did you do that," Rainbow asked bewildered.

"Simple I made a hole in my skin where I insert the key and I hit a button on it and the TARDIS materializes around me." He said pushing his mane into place, "It was a weeping angel defense system at first but now I use it only when I don't have my Sonic Screwdriver."

He snickered it was rare that he didn't have his sonic screw driver on him. Derpy had just become more aware in time to notice the sudden TARDIS appear around them. She got up and stumbled a bit.

"Hey Doc when did you do that thing," she said looking around bewildered that they were in the TARDIS again.

"Derpy it was during a little adventure with a friend," he said.

"Now what," Rainbow asked. She stood jaw open at the amazing technology. "You must need to be an egghead to use this."

"Now we have to go and save Twilight Sparkle," he said tapping his muzzle with his hoof. Derpy knew that all to well. He flipped switches on the TARDIS control panel for a while. Then he hit one button and the TARDIS started to teleport. They heard yelling indicating that the guards had just noticed the blue box. Then all the yelling stopped and they soon appeared in the court room.