"Whoa wait a minute, are you saying Twilight Sparkle is evil?" a very worried Doctor asked.

"Yes," Celestia simply responded.

"THE Twilight Sparkle?" the Doctor asked again

"YES!" Celestia responded again, slightly louder this time

"As in Twilight Sparkle who literally represents friendship and harmony?" the Doctor continued.

"Wait, what?" the Doctor's last comment confused Celestia a little.

"I know, that is my reaction to this mess!" The Doctor exclaimed.

"Has anypony ever told you that you a bit odd, Doctor Whooves?" Celestia remarked, not knowing what to make of him by this point.

"Oh, all the time."

"Well it has been fun, but with Sombra coming I can't have civilians in the castle, it's far too dangerous. Guards please escort him out, I will have your... box returned later

With that Celestia turned and walked out of the dining hall towards the throne room and followed by all but two solar guards, those two stood either side of the Doctor and motioned him towards the exit.

Celestia entered the Canterlot throne room where she was met with six ponies. To the right of the throne sat princess Cadance nervously awaiting what the day would bring. To the left of the throne sat five armoured ponies, elements of harmony hung around their necks, Honesty, Loyalty, Generosity, Laughter and Kindness, only magic was missing and no matter how hard Celestia had tried to find its bearer his or her identity was still a mystery.

"Celestia, what did you find in the dining room?" asked Cadance upon noticing Celestia's entrance.

"Just Ponyville's timekeeper and one of his crazed experiments," Celestia said with a slight chuckle.

"That's all we need, some nutjob blowing stuff up when the enemy is coming to our doorstep!" blurted out Rainbow Dash.

"He's hardly a 'nutjob' darling, eccentric yes but actually quite brilliant. You should see some of his inventions!" argued Rarity

"I'll pass, thank you."

"Now simmer down you two, we ain't got long so the las' thing we need is the two of y'all arguin'," Applejack said to both Rarity and Rainbow Dash.

"I still think we should of thrown them a WelcomeToCanterlotAndHiPrincessCelestia'sNiece Party!" remarked the bubbly and physics defying pony known as Pinkie Pie

Celestia gave a light laugh. "I consider that plan B, Pinkie Pie."

"Well as long as we show Princess Twilight how nice it is to have an aunt like you, your highness, I'm sure everything will turn out OK in the end," said Fluttershy in a rather low voice

Celestia gave a sigh and sat on her throne waiting for the inevitable visit. Next to the throne Pinkie was looking around frantically as she had been since early that morning.

"Ya all right sugarcube?" asked a slightly concerned Applejack

"Oh, I'm fine AJ, it's just I've been wondering if maybe our whole universe is actually fanfiction for a really popular piece of fiction that was initially aimed at kids but was so awesome everypony enjoyed it!" Pinkie blurted with a squee. "Oh and also this morning my Pinkie sense went off in a way I haven't seen before, I think it has something to do with the space time continuum but I can't be sure," Pinkie shrugged

All of the Element Bearers looked at Pinkie in confusion.

"Pinkie, you are so random! Rainbow Dash smirked.

The air grew silent as a carriage pulled by two Pegasi crystal pony slaves flew down from the sky and landed on front of the Castles gates. Out of the carriage stepped firstly King Sombra, indifference etched on his face, following him stepped out Queen Nightmare Moon and Princess Twilight Sparkle.

"You will do fine my little star," Nightmare Moon said softly, giving her daughter an affectionate nuzzle on the head.

The Doctor hid in the shadows to the side of the Canterlot throne room. It had been easy enough to slip away from the guards, he just got them arguing who had the shiniest armor.

The large throne room doors opened with a loud creak as the dark unicorn king stepped in followed by two alicorns.

"Sombra, Luna," Celestia addressed the group with a slight nod.

"Sister," Nightmare Moon responded coldly.

"Greetings Princess Celestia, as we are in a time of 'peace' my wife and I decided it was time you met somepony," said King Sombra

"Sister, meet out daughter and your own niece, Twilight Sparkle," Nightmare Moon ushered the smaller alicorn forwards with her wing and she walked forward until she stood at the head of the group.

The Doctor examined this version of Twilight; she was lavender with a dark blue mane with a lavender stripe going through it, not much change there, she even had the same cutie mark. What was different was the jagged grey crown she wore on her head along with her bright green dragon-like eyes with the telling signs of dark magic leaking from the edges, just like her supposed 'father'.

'What happened to Twilight Velvet and Night Light?' the Doctor had to wonder, whatever the case she was defiantly NOT the dark monarch's daughter, at least not biologically.

"Greeting, aunt Celestia," Princess Twilight greeted indifferently

"Twilight Sparkle, it is a pleasure to meet you after eighteen years of not knowing of your existence," Celestia remarked, rolling her eyes.

"That is why we want you to take care of her for a week, so you can get to know her better," explained Sombra with a maniacal grin on his face.

Celestia's eyes widened at her request and the other six ponies by Celestia shifted around uncomfortably. This was obviously a trap, even the Doctor could figure that out. However, he knew this also provided an opportunity to fix this mess.

"All do respect, but you can't be serious!" Celestia exclaimed

"Not serious? We give you a chance to connect with your young niece, your own family and you throw it back in our face that quickly?" snarled Nightmare Moon as the three dark ponies began to get agitated.

"So she can slit Celestia's throat? No thanks! Go back to your empire!" shouted Rainbow Dash very angrily and even more brashly.

"You dare? I'll have your head, Pegasus!" Twilight shouted back

Both sides became agitated and it seemed they would descend into all out conflict any second, and the Doctor had had enough.

"Everypony STOP!" he shouted out emerging from his hiding place.

Everypony in the room immediately went quiet and turned to the intruder.

"Doctor Whooves, what are you doing here?" asked Celestia, surprise written across her features.

"Who cares? Throw him out Celestia, and we can get back to business," growled King Sombra.

"All of you shut it! I am the Doctor and I. AM. TALKING!"

With that, everypony stopped dead and gave the Doctor their undivided attention.

"Oh look at me getting all authoritative, guess I have that kind of a presence, not surprising when you get to my age I suppose," stated the Doctor a little too gleefully.

The Doctor walked in between the too groups. "Now, Sombra you can't honestly expect Celestia to accept your proposal just like that after everything, do you? And Celestia, losing your temper like that and almost instigating conflict, I know you are better than that! The both of you are acting like children with shiny crowns on their heads, so how about you all take a moment and think about exactly what you want to happen in the next five minutes. Anyway, now that we are civil again I think you should accept their proposal!"

Celestia looked unnerved, what Doctor Whooves was suggesting was unthinkable! Niece or not, Twilight Sparkle would undoubtedly attempt to assassinate Celestia and possibly even Cadance, the dark monarchs were always looking for new ways to take Equestria. However, the Doctor was now looking Celestia straight in the eyes, they seemed old, perhaps older than even her own. His eyes looked as though they had seen wonders she couldn't even comprehend, and horrors that would shock her to her very core.

And for some reason, those eyes made her want to trust him.

"But..." Celestia began

"Well think of it as a cultural exchange, an opportunity for both sides, onwards and upwards and all that!"

Celestia sighed. "I must be crazy, but very well. King Sombra, Luna, I accept and will host Twilight Sparkle for the week. But no more than that."

Nightmare Moon nodded. "Then we shall take our leave."

"Cadance, show our guest to one of the guest suites if you please."

With that, the three dark ponies as well as Princess Cadance all left the throne room.

"All do respect ya highness, but what were y'all thinkin' letting her stay here! You know she's gonna try to kill ya right?" a very alarmed Applejack protested.

"Oh, of course she will Applejack, unless of course you five can show her a better way!" the Doctor said enthusiastically.

"Doctor Whooves, you convinced me to host Twilight, now explain your intentions," Celestia addressed the Doctor with narrowed eyes.

The Doctor chuckled slightly, but then adopted a very stern look on his face as he turned to address the six ponies. "My name isn't Doctor Whooves. It's just the Doctor. I'm a Time Lord, I'm from the planet Gallifrey in the constellation of Kasterborous, I'm over 2000 years old and I'm going to save your lives, and the lives of everypony in Equestria. Got a problem with that?"

The whole room was left in a stunned silence from the Doctor's declaration as they processed his words, and were deciding on whether to believe him.

"He's tellin' us the truth," said AppleJack

"Really darling, how can you be so sure?" asked Rarity.

"My element is honesty, I can see a lie a mile away, and that was no lie."

"Oh come on, AJ. That doesn't make you a super lie detector, you could be wrong!" Rainbow Dash protested.

Applejack adjusted her hat. "Not on this, Sugarcube."

Rainbow groaned, but examined the Doctor more closely. "So... you're an alien, huh?"

"Oh yes! Here, feel my chest where my heart should be."

"Um, what?"

"Oh come on, do it!"

"Um, OK..."

Dash approached the Doctor gingerly and placed a hoof where his heart should be as asked, and sure enough there was a beat.

"Now move your hoof slightly to the left."

Dash did so, there was a second beat, causing Dash to recoil slightly.

"You have two hearts!"

"I do, and that box, it's bigger on the inside and it travels in time and space, it crashed into your dining room due to a temporal anomaly effecting the time vortex."

"I knew it!" shouted Pinkie happily.

"An anomaly, caused by what exactly?" a now even more concerned Celestia asked.

"I don't know, but what i do know is this..."

The Doctor took the time to explain the changes in time, how Twilight wasn't Sombra's biological daughter but was the Element of Magic they had been missing and an Equestrian Princess and how Luna had been redeemed in the true timeline and of course how Sombra was/should actually be dead, along with everything else. When he was finished he waited for the group to take everything else in, it was Celestia who spoke first.

"I remember a case eighteen years ago where a new-born foal, captain Shining Armor's sister no less, was taken. That was Twilight, wasn't it?"

"Yes. Somehow Sombra must of known what she would become, I think whatever caused all this to happen is to thank for that, its manipulation has caused Twilight to be born into darkness," the Doctor replied.

"So, how do we fix it? Change things to how they should be?" asked Rarity.

"Well... after watching how the day is usually saved in Equestria, the elements will be needed, and that means you five befriending Princess Twilight!"

"How exactly are we meant to do that?" asked Rainbow Dash, who was not convinced.

"Start with books, Twilight always has had a soft spot for them, I doubt that's changed," the Doctor suggested.

"This is a great risk you are having us take, Doctor. But if there is a chance to defeat Sombra and get my sister back, as well as gain a student I apparently became so close to, then I am willing to take it," said Celestia in cautious approval.

"Great, you five get to work, Celestia you do your whole 'run the kingdom' thing, and I will work on trying to find out what, or who did this!"

The Doctor turned and ran out of the room, shouting one word as he left.

"Allons-y!"

Author's Notes:

And so it begins...

Next chapter will be a bit different in that it will follow Luna and Twilight and take a brief look at their history in this new timeline.