Courier: Hi everyone welcome to my primary story. This is what Doctor who in Equestria would actually be like in my mind unlike many others where he comes from the BBC universe this time he's 100% pony. This will be season 1 but it's not where near the beginning of the story just the chapters that involve our beloved characters form the MLP:FIM universe

Disclaimer: I own nothing…NOTHING, apart from unique plot and no not that kind of plot…Perverts

NOTE: I prefer to think of the every season to 1 year in MLP so all character from this point are from mid season 2. Also I am changing some events to incorporate The Doctor since this is an AU and it will make for some cool finales.

Doctor Whooves

The End part 1:

Ponyville 1002 CR

It was a beautiful summer's day in the small town of Ponyville and young mare Twilight Sparkle had decided to spend the day out with her friends at Applejacks pond in sweet apple acres after being cooped up for days in her library

"Oh Spike it's such a beautiful day isn't it" Twilight said to her faithful assistant Spike while taking in the suns warmth.

"You can say that again, I can just imagine what Rarity could be wearing" Spike hoped as he walked along side Twilight but both suddenly stopped when a grey earth pony with well-kept black hair blocked their path.

"Like so!" he exclaimed turning his blue tie into a bow tie before walking off.

"What was that about?" Twilight asked raising an eyebrow as the stallion turned a corner and was gone.

"Probably an escapee from the nuthouse" Spike figured before noticing Twilight giving him a sharp unamused glare "what?" Spike added shrugging his shoulders.

"He probably just mistook me for somepony else. I think he'll realise his mistake in a few minutes" after finishing the small trek Twilight walked up to 4 of her friends all enjoying themselves in or near the crystal clear blue water.

"Hi girls, how's the water?" Twilight asked while within ear shot with Applejack raising her hat from under the apple tree giving her the perfect shade.

"Well howdy sugercube, glad you could make it" Applejack greeted before Pinkie leaped off the tree and crashed into the water before emerging for air.

"COME ON IN TWILIGHT! The waters perfect!" Pinkie yelled with Rainbow Dash giving her the evil eyes after being next to Pinkie's impact zone "hehe sorry" she apologised in a modest tone.

"You would definitely benefit from some rays darling you've been cooped up in that library for days now" Rarity added while resting on her deck chair she brought with her "ooh Spike perfect timing could you care to rub some sunscreen on my back?" Rarity asked in a very polite manor.

"Would I! I a…mean of course anything for a friend" Spike almost screamed before rephrasing to not sound too grateful for this rare chance.

"So what were you doing in the library anyway?" Applejack asked as she grabbed a bottle of Cider from an iced crate.

"Well the other day a found a newspaper at my door" Twilight answered laying her satchel down before sitting on the picnic blanket on the ground.

"What's so strange about that?" Applejack replied taking a drink.

"Well its tomorrows newspaper" Twilight replied taking the paper out of her bag to show the earth pony "here take a look".

"You sure it's not just some prank." Applejack added taking the newspaper. Its head line was '15,000 PONIES MISSING! ROYAL SISTERS CONCERNED'.

"I've checked every possible detail of the paper; it's authentic and matches the local paper to the type of paper and quality of ink. What makes it stranger is that ponies have indeed been going missing just not as many as the paper entails and I wouldn't have been none the wiser if I had not read this" Twilight explained as Applejack set the paper down.

"So what now, we on DEFCON 1" Rainbow Dash added as she was listening in.

"DEFCON 1?" Applejack asked confused as she had never heard the term before.

"It's a term used by the military, it stand for defence readiness condition. But in truth I don't know. This is so much like the time I visited myself from the future but that time it was my paranoia that caused the event to begin with" Twilight explained before putting the paper away "so let's enjoy the sun while we can and focus on this tomorrow.

"Darling I'm not one for technical talk but if this paper is telling us of future events then we can't leave it alone. If it does come true 15,000 ponies, that's more than the town's population" Rarity interjected saying they should act as soon as rather than risk the unthinkable.

"I agree Twilight, this can't wait. If ponies are going missing regardless then we can't ignore this" Applejack agreed with her old friend, standing up and adjusting her hat.

"And if there is some big bad behind this then we have the Elements to blast them into a billion pieces" Rainbow Dash also reassured.

"Don't forget the big party afterwards" Pinkie added as Twilight noted in her mind of how lucky she was to have such good friends but then it hit her.

"Wait! Where's Fluttershy?" Twilight asked causing concern to fill the 5 pony's minds.

"I don't know she said she'd be here but I haven't seen her all day" Applejack replied.

"Well we need to find her; if we're not all together then the Elements are useless if we do need them" with nod of confirmation from everyone they packed up and left to find their friend.

After they had split up Twilight had decided to look from the library telescope as it was the best elevation point to spot Fluttershy while Applejack and spike left for her cottage as the rest searched the town, an hour had pasted with not sign of the timid mare but as Twilight was scanning the streets she noticed something odd. She noticed a blue box fading in and out near the high street before it complete materialized and the same grey stallion she met this morning stepped out with a big smile on his face.

"What the hay was that? And it was that pony again…" before Twilight could question it further she heard a knocking at her door and teleported in order to answer it quickly "hello?" Twilight greeted as the local mailmare Derpy Hooves passed her a dark blue letter.

"For Twilight Sparkle" she notified passing the letter to the unicorn before flying off.

"Thank you!" she yelled to the Pegasus as she flew off. Looking at the letter her heart stopped. It was addressed to her but it had her full name, middle name included. The only ponies alive who knew that were her immediate family even the Princess or Spike didn't know. Opening the letter she didn't recognised the handwriting so she knew it wasn't from anypony she knew but she had to know who sent it and what they wanted.

Dear Ms Sparkle

If you're reading this on Thursday of the year 1002. Then that means you've had time to analyze the newspaper sent to you. Normally I don't interfere with events like this but the fate of this planet depends on what you do next. What the newspaper tells you will happen and it will lead to disastrous levels of destruction and you're only hope is to find me before I find them. Please go to the sugercube corner. You'll learn more there.

Good luck Twilight Sparkle.

Yours sincerely

A Friend.

"Sugercube corner? And what does he mean by interfering with events. Whatever the reason whoever this is knows something and I need to find out what!" placing the letter in her satchel and leaving the library she passed Spike and Applejack on her way out.

"There you are? Was wondering if you were still inside. We couldn't find Fluttershy at her home. Any luck?" Applejack asked noticing Twilight in her satchel "uhh sugercube you going somewhere?"

"What? Oh the bag! i got a lead and I'm going to investigate further. Spike continue using the telescope I'm sure we'll find Fluttershy eventually" before either dragon or pony could question Twilights sudden departure Applejack turned to spike.

"Find out where she's going. I know when she's hiding something and that never is a good sign".

Sugercube corner

Walking into the bakery Twilight was surprised that nopony was in here, despite the shop sign stating it was open. Pinkie was most likely still searching for Fluttershy but still the cakes should still be around.

"Hello, is anypony here?" Twilight called out unaware she was being watched as she passed the counter to the kitchen "look you sent this letter to me and I want to know why?" Twilight called out again hoping to get an answer with the shop being dead quite the unicorn jumped when she heard a sound similar to the one her teleportation spell makes down in the basement. Slowly walking down the wooden steps Twilight used her magic's light to illuminate the room and nothing was different from the last time she was down here. But she was sure she heard something and begun to look around "somepony down here?" Twilight yet again called out before accidently knocking down some metal trays as she began to pick them up another still on a table fell again knocking into something in front of the unicorn giving the distinctive sound of metal on metal as she stopped in fear whatever was standing in front of her completely invisible suddenly revealed its self and as the unicorn slowly looked up she was almost blinded by the bright blue light on its chest before being met with a cold metal face with two black holes for eyes "oh my Celestia!" Twilight yelled taking several steps back as the metal pony took a couple forwards.

"Scanning…designated species Equine, subspecies Unicorn compatibility 100 percent" the metal pony said in an emotionless electronic voice.

"What are you?" Twilight asked too scared to be able to concentrate for a teleportation spell.

"I am designated generation 4 Cyberform 303, previously known as Cup Cake. You will be upgraded to Cyberform 1009" what Twilight just heard was absurd she just heard this thing identify itself as Mrs Cake but unable to think clearly about it Twilight screamed as two cables came from the metal ponies back one of which had a built in taser but before it could strike a metal clank could be heard that attracted the creatures attention, it was a small black cylinder that attacked itself to the hull of the machine before activating sending an electric pulse throughout its systems "Systems compromised! electromagnetic field detected!".

"yea sorry about that but I can't let you touch her like you've converted so many others" a familiar voice was heard from the stairs leading upwards and after stepping into the light of Twilights magic she instantly recognised him.

"YOU!" Twilight yelled confusing the stallion.

"Me? You recognise me then. Why am I not surprised, I never meet people in the right order" the stallion replied with a fun smirk.

"What are you talking about?" Twilight asked before the machine began to scan him.

"Scanning…" it began with the stallion looking to the unicorn with his smile turning to an angered expression.

"I would run if I were you, it's not going to be immobile for long and I'd rather not let it find out who I am" the stallion recommended as Twilight was still too frightened to move "NOW!" after feeling the authority in his voice Twilight without hesitation sprinted past him and back up to the bakery.

"Designated species…Unknown, biometric scans identify Two hearts" the machine deduced as its cables began to move again.

"I'm so Sorry Mrs Cake; I'll make sure your kids are safe" the stallion apologised with a sad expression before leaving.

Just outside the bakery Twilight charged out of the doors at such a speed she crashed into Applejack.

"What the hay Twilight!" Applejack yelled before noting the terrified expression on Twilights face "Twilight what's wrong? You look like you've seen a ghost" Applejack asked before the grey stallion Twilight saw twice before also sped out of the bakery but instead of crashing into the two mares he leaped above tem landing just behind them before pulling out a small stick shaped device made from copper. Pointing it at the door to sugercube corner the door shut on its own locking immediately afterwards "and who the hay are you!?" Applejack demanded as he was emotionless unlike her friend.

"I'm The Doctor and I'm you're only hope" he answered as he adjusted his tie.

Next Time:

The End Part 2

Courier: thanks for reading and please tell me what you think in the review section, I would like as much feedback as possible.

This is the first episode to a rebooted series that I called The Equestrian Chronicles. Due to choices I made it worked as a fun project but not as a well made story so this should give it that darker feel that doctor Who should have with a bit of pastel coloured ponies to boot.