The Doctor

by PinkiePieParty055

Rating: everyone
Tags: Princess Luna, Adventure, Crossover, Twilight Sparkle, Princess Celestia, My Little Pony: Friendship is Magic, Doctor Whooves, Sad, Main 6
Length: 3333

Doctor Whooves and Twilight save Equestria.

My name is Twilight Sparkle. I travel with the Doctor but, Equestria is in danger. Mysterious creatures traveled to Canterlot. It's up to me, my friends, and The Doctor to save Canterlot and Equestria.

Published 2014-07-18 00:30:05 UTC
Last updated 2014-07-18 00:30:05 UTC

1. The Blue Box

1. The Blue Box

There in Canterlot Castle the Royal Sisters were arranging the First Moon Celebration."Luna what shall we do for the First Moon" said Princess Celstia in a soft soothing voice which calmed Luna. "Since thou has not been to a celebration we think thou should-" She stopped as a Canterlot guard interrupted. "What thou meaning of this" said Luna. The guard bowed to Luna "Sorry for the interruption but Princess Celstia" he turned to Celstia and nodded. Celstia gasped and then closed her eyes and nodded.

"Luna...I want you to stay here" said Celstia firmly.

"Tia" Luna then glanced at the guard she had realised that she was addressing Celstia as Tia. She could tell that this was serious."I mean Celstia what is thou suppose to do"

"Guard and protect Equestria" Celstia had looked at her sister and looked almost at the verge of crying.

"Tia is there something the wrong?" Luna said with a worried tone in her voice. She did not care that she addressed her as Tia this was her sister. Her sister meant a lot to her she wanted to know what the problem was.

Celstia was silent she hugged Luna and turned away. Luna could tell Celstia was crying. Celstia and the Canterlot guard left. There Luna sat confused, worried, and lonely. Luna ~~thought~~ she knew something was wrong and she was going to figure it out. Luna thought: Something is wrong and I want to know what

While in Ponyville

Twilight was in the her library reading."AAAAAAAAAAAAAAAAHHHHHHHHHHHHHH" the scream had made Twilight jump.

"Spike!" Twilight had called.

"Yes" Spike said coming from upstairs.

"Phew you are ok" Twilight said with relief.

"Why wouldn't I be?"

Then, Twilight's pupils shrunk. She had realized that there was a mare in trouble.

"Spike I'll be back" Twilight said. Before Spike could reply Twilight was gone.

Twilight was outside it was night so everypony was asleep or at home. She looked around everything looked normal she turned a corner there was a Pegasus statue cuffing it's hoofs in front of it's face. In the middle of the alley. "AH!" A little startled "Oh it's just a statue but ,how did you get here?" Blink! The winged statue had stopped cuffing her hoofs over her face but now it got closer and more vicious looking with sharp teeth showing and reaching out for her. "AAAAHHH" she screamed. All of a sudden a brown stallion jumped in front of her."Don't Blink" he said.

"Why?" Twilight asked.

"I will tell you if you don't blink!" He said in a very serious tone.

Twilight did as she was told and she didn't blink.

"Are you good at magic?" He asked.

"YES" Twilight said with excitement and also with a little sarcasm.

"Shoot it" he said.

She did, shooting a purple blast of magic. After the smoke cleared it was still there.

"You can't kill stone"

"Oh no, what do we do?" she said staring straight at the statue.

"Don't Blink" he said pulling a device out of nowhere. He buzzed at the creature the creature seemed to.....well be erased.

"You can look" he said with smile. After blinking her eyes a couple of times, she looked at him.

And yelled "Now who ever you are you are going to answer like WHAT WERE THOSE THINGS?!"

He said calmly "Those are the Weeping Angels or Weeping Pegasus"

"Thank you and can you answer my other which is WHO ARE YOU, WHY COULDN'T WE BLINK, HOW MANY ARE THEY,AND WHAT DID YOU DO TO IT?!!"

He then explain who he was,and about the Weeping Angels .His name was The Doctor and he was a Time Lord. Then, he got into detail about the Weeping Angels.The Number One Rule : Don't Blink. Blink and you are dead. They send you back in time and and feed on your time energy. He told all about the sonic screwdriver which turned the clock back to the statue so it never existed and basically do anything. After he had cleared it up to Twilight. She was shocked, amazed, confused, and a huge rage of different emotions.

"So your telling me you are a Time Lord?"
"Yes" said The Doctor.
"Prove it" said Twilight with a smirk.
"Follow me" he said. They approached a Blue Box that on the top read 'Police Public Call Box'. "Is this a joke?"
The Doctor sighed hoof smacking himself in the face. "Just come in"
"Fine"
She walked in and she was shocked."It's..It's"
"Bigger on the inside" he said with a smirk.
"No, it's impossible" Twilight said amazed."Did you do it? I have not seen any spells for this"
"Good old TARDIS it's a abbreviation for Time and Relevant Dimension in Space" he said.
"Yeah" she said in disbelief.
"Do I still have to prove it?" He said.
She turned and looked at him with a smile and said "Yes"

"Allon-y!" He said with glee.

With that the TARDIS started to shake and twist. After that he opened the doors and they were on the...."MOON!" Twilight yelled.

"Yep the moon she is pretty" he said.

"I still don't get how this is possible without magic"

"Nothing is impossible"

" Where else can we go?"

"Anywhere" The Doctor said.

"Let's go somewhere" she said.

"Where?"

"Surprise me"

Author's Note

This is my first story hope you like it :)

2. Adventure

Luna was in deep thought about Celestia. So many questions popped in her mind. What did the nod mean? Where did she go? But, most important question to her was: Why?. Luna decided she wanted to find out herself. " Masquerade" she called.

"Y-Yes princess" said a yellow earth mare with a blue mane.

"Thou-" Luna stopped to correct herself. "I will be out for awhile"

"P-Princess if you don't bother me asking where?" Masquerade said.
Luna was almost out of the door but heard the question. She stopped and turned around and said "uh....The Garden!" With that she decided to search there.

She trotted to the Royal Garden. She had searched everywhere there was nothing. She was about to leave until. Swoosh! Luna turned around to see a tall shadow with sharp teeth.

"AAAAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHHHHHHHHHH"

Meanwhile with The Doctor and Twilight

"Close your eyes" said The Doctor.

"Ok there closed" said Twilight as she pulled the Doctor's hooves off of her face.

After a couple of whizzing and crashing sounds. She could hear him opening the doors of the TARDIS.
He had taken her hoof and walked her out of the TARDIS.
"Open" said the Doctor taking his hoof off her's.

"Wow!" she said amazed
.
"Welcome to the Aurora Light City!" said The Doctor with excitement in his voice.

"I want to check it out and what is wrong with that pony?" she questioned with curious. As a stallion walked by but he was clear like glass but liquidity.

"They are the water ponies they are made out of of water" he said "By the way they are incredibly nice"

"What do they do?" she asked.

"Same things we do only they earn special orbs that..uh.... help them stay in one piece" he continued " They age like me"

"How old are you?"

"903 years old" he said with a smile.

"Wow" she said a little shocked.

"They have a Princess her name is Crystal Aurora she is very beautiful" The Doctor sighed.

"Is there something wrong?" Twilight asked in a worried tone.

"I tried to save her mother" he said looking at the ground.

"Her name was Diamond Crystalline Light. She a magnificent water coat with a special blue silk that was emended in her hair. The Broken Eyes were planning to steal the orbs to take form. Many of them took shape but I took the orb from them. After I defeated them, she used the last orb with all the magic she could and she scattered it to all of the water ponies. But, there weren't enough since she had used all of her magic she was very weak a regular one would not work and there no full orbs left. I had tried the Crystal Orb but she was all ready gone an it her place was the tiny filly Crystal Aurora and so when the King: Golden Spiral came and found us and I told him what happen. Golden Spiral was a regular unicorn golden pony his cutie mark was a Spiral Galaxy,his coat was gold, and his mane was yellow with a second color of gold"

"So she is dead" said Golden Spiral.

"Yes and I am so very sorry" The Doctor said in a very sadden voice. "She left a filly" he said with a slight smile.
Golden Spiral looked down to see a small sleeping filly with a flash of rainbow. The Doctor gave the sleeping filly to the King. Doctor flashed a smile and then turned to the TARDIS and left.

Golden Spiral thought: Doctor?

"I am so sorry" Twilight said while stroking the Doctor's Back.

"Never mind that let's go see Princess Crystal" he said brightening up.

"AAAAAAAAAAAAAAAAAAAAHHHHHHHHHHHHHHHHHHHHHH"

"THE PRINCESS!!!" They yelled.

They both went into a full gallop and both ran into the water like castle into the Princess's room. There in the corner sat the Ailcorn Princess, guards laying on the ground unconscious, and The King on the floor next to the Princess unconscious. In front of her was eyeless black shadow crawling from the floor to her. She turned to the Doctor and whispered "Help". The shadow had turned around and saw The Doctor and with vicious teeth it crawled to them.

"Well we meet again" he said.

"Give us land and POWER so much POWER" it said very demanding and threatening.

"So you can talk you evolved " with that he said he pulled out his sonic screwdriver and beamed it at the monster hurting it. With that it made it very mad and it got closer then it stopped and smiled evilly showing it's teeth.

"DOCTOR" Twilight said pointing to two shadows appearing beside the first shadow and the other side. The first shadow had taken form while the others were still on the floor.
"How can you take form?!" The Doctor said very firm.
"We found new power and this is only the beginning" it said as it and the other shadow faded away.

Twilight walked around The Doctor to the Ailcorn Princess. She was shaking and crying. Twilight went up and held her.

"Thank you Thank you so much" said the Princess smiling while crying.

"Your welcome" Twilight said in a very soothing and calm voice still holding her.

"T-Those things what are they?" said the Princess trying not to cry.

"The Broken eyes" said The Doctor walking up to her."Can you tell us what happened?"

"Well o-ok" She said

"I was in the castle looking out the window and then my father came running upstairs were I was. He said something about running from some things. After that he closed the door and blocked it with a spell. He sat me in a corner and was standing in front of me with his horn out. He told me "What ever happens to me, you fight for our city" Then I heard a smash and the door burst open and the guards were thrown. My father tried to use his magic but those things drained his magic and then throw my father aside and that's when I screamed. The thing acted strange toward me it's like there was a shield around me then it was about to do some type of magic that when you came and that's what happened."

"Doctor how can they drain magic?" said Twilight.

"I don't know" he said. With that he thought:"We found new power and it's only the beginning".

"So Twilight I think it's time for you to go home" he said.

"What about me?" The Princess said getting up.
"Oh right" he said and pulled his sonic screwdriver and scanned The King and guards."Their unconscious but, fine take them to the nurse and there're alright " he said walking out. Twilight who was following said "Bye hope to see you again without something scary happening"

The TARDIS made some whizzing and crashing noises then it stopped.

"Here we are Twilight, home safe and sound" he said with a smile.

"We should this again" she said "Without the crazy."

"Crazy is everyday" he said "Do you want to travel with me?"

She smiled and said "Yes"

He said " See you tomorrow" and he walked into the TARDIS and it started to fade and then it was gone.

She turned around ,smiled and opened the door where Spike jumped onto Twilight and said "PRINCESS CELESTIA AND PRINCESS LUNA ARE MISSING!!!!!"

Author's Note

Did the second chapter :)

3. Run!

Twilight jumped off of Spike as fast as a blink.
"WHAT!" Twilight yelled. It could be heard though all of Ponyville."Where are they?!"
"That's the thing Princess Cadence requested that you and all of the Elements of Harmony to come to Canterlot quick!"
"Then come on!" she said grabbing Spike.

Twilight rushed to her library she had informed the Elements of Harmony to come to the library.
She soon heard hoofsteps and then a knock. She opened to the door to see 6 ponies."Darling, we heard what happen is there something wrong" said a white unicorn with a purple curled mane and had 3 diamonds as her cutie mark.
"Rarity there is something wrong come in" Twilight said as she lead Rarity inside.

After that a pink-maned earth mare with 3 balloons, a rainbow-maned Pegasus mare, and a yellowed-maned earth cowgirl came in.
"Where is Fluttershy?" asked the rainbow-maned Pegasus mare named Rainbow Dash. As soon as words those were said a light yellowed mare walked in. "H-Hi Twilight"

"Good now everypony is here I half to tell you that CELESTIA AND LUNA ARE MISSING" she said.

Everyone gasped."That's right and it's up to us to find out"
"Ain't the next train to Canterlot in a hour" said the country girl named Applejack.
"Right everypony, we meet at the train station in a hour" said Twilight confident.

At the Train Station

"Everypony here Rainbow Dash, Fluttershy, Pinkie, Applejack, and Rarity" she said. All nodded. "ALL ABOARD" announced the conductor. All of the ponies boarded. Applejack sat by Rarity, Pinkie sat by Rainbow Dash and
Twilight sat with Spike. "I can't wait to go back to Canterlot" Rarity said very eager.
"Remember Rarity this is a mission, not a shopping trip" Twilight said firm. Rarity pouted. Everypony laughed. "What?" she whined.

*1 Hour later*
They were getting closer to Canterlot. "Alright everypony we are here to find Princess Celestia and Princess Luna". Everypony smiled and nodded in agreement. The train screeched to a stop.The door opened in front of them was a pink Ailcorn Princess with a yellow,pink,and purple mane. "Twilight" the ailcorn said as she trotted over to her and hugged her with a smile. After, her hug a white unicorn stallion with a light blue and regular blue mane. "Twi Twi" he said walking up to her. "Cadence and Shining Armor what happen?" Twilight asked. Cadence smile faded away into a frown. "The Princess are missing Luna was last heard going into the Royal Garden and Celestia we don't know" she said looking down. Shining Armor put his hoof on her to comfort her. "We are on a full search for them"
"We'll help search in the garden" she said confident.

"Thank you we need all the help we can get" Cadence said with a smile but back down to a frown. "But sadly me and Shining haft to go back to the Crystal Empire it's in your hoofs now Twilight"

"It's getting dark I'll get a guard to your luggage now go rest, we have a train to catch" Shining Armour said. "Good Luck Twily"

While in her room Twilight thought: I wonder what happen to Celestia and Luna
After, thinking for a moment she heard the TARDIS landing and turned around and there was the TARDIS. The Doctor came running out.
"Twilight something very bad is-" he was interrupted by a scream.
"That's Rarity" she said. Both of them ran out to see Rarity frighten by none other then the - Weeping Pegasus.

"Rarity don't blink" Twilight yelled. With evening looking Rarity did as told.
Soon the others came. "What the hay is that?!" Applejack said pointing at the creature.
"It is a Weeping Pegasus don't blink or look away" The Doctor said.
Twilight turned around to see 3 more Weeping Pegasus. "DOCTOR!" Twilight yelled. The Doctor turned around and said "Twilight use your magic face them at each other" he said. She nodded and a purple magical aurora surrender her horn and she moved the statue but, it was very difficult. After that the statue turned into a shadow faded away.

"First, WHO ARE YOU? AND WHAT ARE YOU DOING HERE?!?!" Rarity said.

"Well I am the Doctor just the Doctor and Twilight travels with me and that is a long story" he replied.
"Ok Doctor how long have you and Twilight...traveled?
"A day" he said.
"Oh did you go to Prance?" Rarity said nudging him ,making him blush.
"Oh no we went to Aurora Light City"
"I have never heard of such it's sounds amazing"
"It is...in the 4th dimension" he said. Rarity looked at Twilight, Twilight nodded.

"What?.....how?..."She and the others were shocked expect for....Pinkie and Twilight.
The Doctor rolled his eyes "Let me explain-". He was stopped by Pinkie.

"You are a Time Lord that has a magic box that can go anywhere but you're here because the Princesses are gone and you're to help too" After that Pinkie smiled.
"How did you?..." He looked at Twilight and she shuck her head.

"Do you really think I would believe you?" said Rainbow Dash dashing to him. There faces were inches apart.
"What about the those shadows?" He said pointing to the shadows.
The shadows crawled across the floor to them. Then, he realised they were The Broken Eyes
"What are you doing here?!" The Doctor said to the shadows.
"WEEPING PEGASIS!"yelled Rarity. She pointed to behind the shadows and there were 4 statues.

"We are the Broken Eyes and we have found Power here by Princess" The leader of the Broken Eyes said.

"Where are Princess Celestia and Princess Luna?!" Twilight demanded.

"They are magic and now Ours" it said. After that they disappeared and the statues were remaining.

"Twilight use your magic" he said.
A magenta aurora glowed from her horn, but nothing was happening.
"Twi why is nothin happening" Applejack said still watching the statues.
"My magic is not working" Twilight said.
They all focused on the statues......Except Pinkie she was making funny faces to it.

"Doctor, what do we do?" Twilight asked still looking at the statues.

He smiled and said "Run"

They all ran, Twilight looked turned around to see the statues but, they weren't there. She stopped. Everyone stopped and looked at Twilight. Then, they noticed that the statues were gone."Good now to go get the Princesses, Twilight come on we need the TARDIS" taking Twilight by the hoof. "Wait a minute, were coming too" Rainbow Dash said. The Doctor nodded. They came to Twilight's room, they walked over to the TARDIS.

"Is this a joke, because we can't fit in it" Rainbow Dash said.

Twilight rolled her eyes and walked in with The Doctor and Pinkie Pie who hopped in. The rest shrugged and walked in. They were shocked at the discovery......expect for Pinkie as usual.

It was Bigger on the Inside

Author's Note

The chapter might start coming a little slow.