Doctor Whooves: Born Into Darkness

by tom117z

First published 13th of August, 2015

The Doctor had been in Equestria for a year and in that time he has seen wonders, but what happens when something, or someone changes Equestria's history and only the Doctor is aware?

One year ago the Doctor landed in Equestria after falling into some sort of rift. There he met new companion and friend Derpy while taking the guise of Ponyvilles timekeeper 'Doctor Whooves'. But one day while planning a trip to the past something happens.

With time changed and a mysterious but familiar force pulling the strings from the shadows can The Doctor save the day and fix the timeline?

The key to doing so may lay with Twilight Sparkle, but the she's not the Twilight the Doctor knows.

Cover image source:
http://darkflame75.deviantart.com/art/Doctor-Whooves-and-his-TARDIS-UPDATED-445060336

1 - Prologue

Location: Earth
Time Frame: October 1st 2016

Two figures stood at the top of the Eiffel Tower, leaning over the railing to get a good view of the city, behind these two impossible figures stood a blue box.

"So Doctor?" Clara asked. "What else is out there?"

"Oh all sorts," responded the Doctor

By this point in his life the Doctor was over 2000 years old and in his 12th/14th incarnation, depending on whether you count the War Doctor and the Meta Crisis 10th Doctor. In this form, he was a greying Scotsman but still had the same childlike spirit under the gruff exterior.

"There are even things beyond our own universe," the Doctor casually mentioned.

Clara turned to look at the Doctor. "What? Like parallel universes? I mean I know about the infamous 'Pete's World' and their Cybermen, but how many universes are there exactly?"

The Doctor now turned to look at Clara, that childlike glee glowing in his old, old eyes.

"Who knows? Billions upon billions, possibly even infinite, every choice leads to branching paths, every piece of fiction creates a new universe based around that fiction, reality is a large place, and well... maybe we will end up in one such universe one day, my travels have taken me to many strange and wonderful places, but I bet there are still things out there that will surprise me yet".

10 months later
Location: Ponyville
Time Frame: 1784th year of Celestia's reign.

The night was peaceful, Luna had brought out the moon and arranged the night's stars to her liking. Along a dark tattered lane, a lone figure slowly trotted towards the town. The figure was equine in nature, with grey fur, a blonde mane and tail along with some slightly mismatched eyes. Derpy stretched her wings and let out a yawn, it was most certainly time to return home where her daughter was waiting, despite this Derpy stopped and looked up at the stars in the night's glorious sky. She couldn't help but wonder what was out there... Other life? Other planets?

Derpy let out a sigh, she knew she would never know, in their day and age it was impossible. However, sometimes the impossible does happen if you are in the right place at the right (or wrong) time.

A loud bang echoed throughout the night sky almost making Derpy fall over in surprise, a large rift opened as a wheezing sound began to vibrate throughout the environment. Then a fireball emerged from the rift, the anomaly closing behind it. With an almighty crash, it impacted just outside the Everfree Forest.

Derpy rushed to the impact site wondering what the hay just happened, when she arrived she saw a large charred crater, in the centre on which was a badly burned blue box marked 'Police Public Call Box'.

"Whoa," muttered Derpy as she cautiously crept towards the mysterious and impossible object.

Suddenly the doors opened and a heavily injured bi-pedal creature staggered out, himself being incredibly burned and with several open, bleeding wounds. From what she could make out the creature seemed to be getting on in years, it had grey hair on its head and eyebrows which looked like they could open bottles by themselves. The figure looked at Derpy with a serious expression on his face.

"I would get back if I were you, what comes next is extremely volatile," the figure said.

Derpy, unaware of the TARDIS' translation matrix was surprised the that the creature spoke fluid equestrian, but nevertheless did as it asked and retreated to the edge of the crater.

"Thank you," said the figure, resigned to his fate.

The figure began to glow a brilliant gold that soon enveloped his entire body, before exploding outwards with such force that Derpy was instantly knocked to the ground. When the explosion stopped Derpy slowly got up and looked into the crater's edge, where the bipedal figure once stood was now a brown coated stallion with a darker brown mane and tail. His cutie mark was that of an hourglass.

The figure looked up at the dumbstruck Derpy and stated, "Hello, I'm the Doctor, now listen to me very carefully and answer one very important question!".

Derpy slowly nodded and said: "Okay," with a slightly shaken voice.

The Doctor smiled and asked. "Am I ginger?"

One Year Later
Location: Ponyville
Time Frame: 1785th year of Celestia's reign.

The Doctor had settled well into Ponyville with the help of his friend and companion Derpy. In the past year he had seen extraordinary things from magic to the coronation of Princess Twilight Sparkle who is another friend of the Doctors, though only Derpy is aware of the Doctors true past, and finally most recently a parasite called the Tantabus had infected everyone's/pony's dreams in Ponyville, and in said dream he almost got crushed by a living house! The Doctor has been loving every moment of his time in Ponyville, so much so he hasn't even made a trip through time and space since arriving, though he has promised Derpy that he will take her on a trip one day. In Ponyville he went under the name 'Doctor Whooves' as a play on his old favourite question 'Doctor Who?'. He also serves as Ponyville's timekeeper, meaning he is in charge of keeping the clock tower up and running as well as keeping the time during events such as 'Winter Wrap Up'.

The Doctor trotted through town towards his home and workshop where he performed experiments mixing time travel and magic, he was still a little disappointed he regenerated into an Earth Pony and not a Unicorn or Pegasus but regeneration is a lottery after all.

"Hey Doc," sounded a familiar voice.

"Princess Twilight Sparkle, your most benevolent highness," the Doctor responded to one of the four alicorn rulers of Equestria.

"Oh come on you know I don't like friends referring to me as 'Princess'," said Twilight, a little annoyed.

"Well I don't like being called 'Doc'," the Doctor retorted with a smirk.

"Well fair enough I guess, where are you heading off to anyway? Twilight said curiously.

"Oh just heading back to the workshop for some, er... timey wimey stuff," the Doctor said cryptically, he couldn't tell her about his plans to take Derpy back to Ponyville's founding next week.

"Cryptic as always," sighed Twilight. "Anyway I've really got to get back to the castle, the map is apparently highlighting something, an immortal princess' work is never done."

"Yeah, I know what you mean... Or at least about the immortal thing, not the princess thing, well actually saying that there was this one time... ah, actually never mind that I've got to get moving. See ya later, Twilight!" the Doctor said before hurrying off, leaving behind a slightly confused Twilight.

"There is definitely something odd about that pony..." she muttered to herself.

The Doctor reached his workshop and closed the door with a bang, once again he almost revealed his true nature through his ramblings. He had already decided he would tell the princesses of his identity, but not yet.

"Derpy? Are you here?" The Doctor shouted, getting no answer.

The Doctor wandered through his lab towards a seemingly barren wall, when at the wall he removed a secret panel to reveal a large switch that, when activated, caused the wall to slide away and reveal a hidden room where a familiar blue box laid in wait.

"Hello old girl," the Doctor greeted happily as he walked into the TARDIS.

The control room had been reverted back to its coral design with grates lining the floor's, big coral pillars reaching into the ceiling with the central console glowing a vibrant green around the controls. Of course, the controls themselves had been modified to be better used by a being with hooves and not hands. Oh and round things lined the walls, plenty of round things. The reason for him going back to the coral design was that this new regeneration of his seemed to have his 10th self's personality, just a little ponified.

The doctor walked up to the console, on said console there sat a band which he slipped onto his left foreleg, onto this band was strapped his sonic screwdriver, still sporting the same design its had since his 11th self. One thing that still perplexed the Doctor was that he seemed to be able to pick up objects like the sonic with his hooves, the laws a physics in Equestria were certainly odd.

Then the cloister bell rang out.

The Doctor looked around in worry as the bell continued to ring, signifying some sort of temporal emergency. The Doctor brought round the consoles monitor and observed the readings on the display.

"History's being rewritten!" the Doctor exclaimed in panic.

Suddenly the whole TARDIS shook violently as it dematerialized itself in an attempt to protect them from the temporal anomaly. Several round things exploded and part of the console burst into flames as the TARDIS continued to be rocked throughout the changing time vortex.

"Oh come on old girl find us a safe place to land!"

Suddenly the shaking stopped and the TARDIS began to materialize in a new location. The Doctor looked at the display and observed they were still in the right time period, only a few seconds since he entered the TARDIS in Ponyville in fact, he also seemed to be in Canterlot Castle and the unstable re-materialization had left a slight hole in the dining room wall.

"Whoops," remarked the Doctor, well if he was going to tell the princesses the truth now was probably the time.

Outside Canterlot a hooded figure watched silently as his plan fell into place. All the chaos of this new timeline would empower him for centuries! And this new unsuspecting world had no idea he even existed, that rift had led him to a new universe ripe for the taking, and he would soon feed.

Scanning over more of the display The Doctor saw the TARDIS had taken severe damage and wouldn't be moving again for a while.

Sighing the Doctor left the console behind and exited the TARDIS, only to be met with several angry looking solar guards and a bemused looking Celestia.

"Doctor Whooves what is the meaning of this? And what is this box exactly?" Celestia asked in her usual calm tone.

"Oh that, well funny story that you see..." the Doctor started before Celestia cut him off.

"Actually, tell me later! The rulers of the Crystal Empire will be here soon and I have to make sure security is at its best, I don't trust them not to try anything even for an occasion such as this," Celestia hurriedly remarked.

"Rulers of the Crystal Empire? You mean Cadance and Shining Armor?" asked the Doctor as the cogs in his brain began to turn.

"Cadance an...? No, King Sombra and Queen Nightmare Moon!" responded Celestia.

At that the Doctor face fell as the cogs in his brain began to turn faster, realisation dawned upon his face as he figured out what the anomaly had done.

One of the solar guards approached Celestia. "Your Highness, why are the dark King and Queen coming here?"

"To introduce me to somepony," She responded, before turning to address the rest of the ponies in the room.

"Their daughter and my niece, the dark princess Twilight Sparkle!"

"Twilight?" the Doctor muttered as his face formed a look of pure horror, this was going to be a long day.

Author's Notes:

So here is the prologue to my first story on FIMfiction, hope you enjoy it! :D

Video was made by CShep99

2 - Things Have Changed

"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.

3 - Born Into Darkness

Location: Canterlot
Time Frame: 1767th year of Celestia's reign

Two solar guards walked down a quiet street in the dead of night, not noticing a shadow watching them go past. Nightmare Moon crept towards Canterlot Hospital not letting anypony even catch a glimpse of her. Her target was a new-born filly named Twilight Sparkle, her husbands mysterious 'benefactor' had told them that while this filly would be used as a weapon against them in the future, if she were to be corrupted she would prove a valuable asset to them that may shift the balance of the war in their favour.

Or at least that's what Sombra claimed, he has never revealed the 'benefactors' identity to anypony, a fact Nightmare Moon found slightly disconcerting.

Walking carefully through the mostly empty halls of the maternity ward she spotted her destination. Stealthily entering the room Nightmare Moon observed the soundly sleeping form of Twilight Velvet, next to her was a specialised unit holding Twilight Sparkle. Her heart melted when she saw the cute sleeping filly, Nightmare Moon had wanted a child for some time but Sombra had always been opposed to it.

"It's just a shame it had to happen in such a regrettable way," muttered Nightmare Moon to herself, briefly glancing at Twilight Velvet while approaching the filly. Using her magic she slowly opened the unit up and gently picked up the filly. With Twilight Sparkle secured she left the hospital and headed back to the Crystal Empire, trying not to dwell on the family's heartbreak that would occur the following morning.

Location: Crystal Empire
Time Frame: 1777th year of Celestia's reign

Today was her daughter's birthday. Princess Twilight Sparkle was turning ten years old. The past ten years had been the greatest of Nightmare Moon's life, she had come to love her 'adopted' daughter greatly and couldn't be prouder of the mare she was becoming. However one concern she did have was Sombra, he had always been distant from Twilight and Nightmare Moon suspected that he viewed her as nothing more than a tool, an eventual weapon against Celestia. A concept Nightmare Moon found incredibly troubling.

She approached the palace library, where else would her daughter be? She placed a hoof on the large doors and pushed, opening them with an almighty creak.

She saw her daughter in the corner so engrossed in a book she hadn't even noticed Nightmare Moon enter. Nightmare Moon just stood there and observed the lavender Princess for a moment. On Twilight's flank existed a starburst cutie mark she had gained only a couple of years ago, a rare sonic rainboom had exploded throughout the sky, startling Twilight so much she had an outburst of magical energy that turned several guards into Cacti before Nightmare Moon was able to calm her daughter down. Those Cacti still decorated the hallways to that very day.

Nightmare Moon calmly walked up to Twilight and stood behind her, slowly she leaned down and simply whispered into her ear, "Hi."

Twilight jumped high into the air with a deafening shriek, dropping her book in the process. The unicorn turned to glare at her mother, who was laughing so hard she had fallen onto the floor.

"Not funny mother!" Twilight shouted while using her magic to fling her book towards Nightmare Moon. "Now I've lost my page...".

Nightmare Moon stopped laughing so hard and sat up, looking directly at her daughter.

"Do you even remember what day it is, Twily?"

"Um..." muttered Twilight simply, racking her brain thinking that maybe she had indeed forgotten something important.

Nightmare Moon chuckled, using her magic to levitate a wrapped gift towards her daughter. "Happy Birthday, my little star".

Twilight's face brightened instantly at the sight of the gift, which was book shaped, her favourite shape when it came to gifts.

"What is it what is it?!" shouted Twilight excitedly.

Nightmare Moon just sat there grinning as Twilight jumped onto the gift and ripped off all the wrapping paper in seconds revealing...

"Daring Doo and The Castle Of Doom!" shrieked Twilight. "But this isn't even meant to be out for another two months!" she stated hugging the book tightly to her chest.

"That's not all, look at the bottom."

Twilight did as directed, examining the writing at the bottom of the book in wonder. "And its signed by A.K. Yearling herself!" shouted the extremely happy young filly, who preceded to almost tackle Nightmare Moon in a strong hug.

"Thank you! Thank you! Thank you!"

"Anything for you my precious daughter," cooed Nightmare Moon, nuzzling the top of Twilight's head. "We also have one more surprise for you later, it may not be as exciting as 'Daring Doo', but I think you will still like it!".

Twilight nodded at her mother. Both mares then proceeded to sit down and began to read the new book together, Nightmare Moon cherishing every moment of Twilight's happiness.

During this Nightmare Moon thought to herself, 'In a few hours Twilight's next surprise will be revealed, and Twilight Sparkle the unicorn will cease to exist, while Twilight Sparkle the alicorn will be born'.

Nightmare Moon nuzzled her daughter's head again, at this moment considering herself the proudest mother on Equus.

Location: Canterlot Castle
Time Frame: 1785th year of Celestia's reign

Twilight sat at her window looking up into the sky, thinking of happy memories she had with her mother, the quicker she was done with Celestia the quicker she can be reunited with her.

Twilight Sparkle was surprised that there were no guards left at her door, even more surprising was that there was no magical surveillance surrounding her anywhere. Either Celestia was getting sloppy, or she was up to something. Twilight couldn't help shake the feeling it was the latter, but then again Twilight had a habit of overreacting to things.

'Not that it matters...' Twilight thought. 'By weeks end Celestia will be dead and Equestria will follow suit'.

Twilight turned away from the window and approached her luggage, she began to unpack. Among the things she had brought with her were her Smarty Pants doll she's had since she was small, and her entire collection of Daring Doo books. She picked out 'Daring Doo: The Castle of Doom', sat on her bed, and began to re-read it for the 1000th time.

Several minutes later there was a knock on the door.

"Enter," Twilight called out begrudgingly.

A brown coated stallion entered, he had a darker brown mane and tail along with an hourglass cutie mark.

"Sorry to barge in on you like this Twilight, I was on my way to do some, er... research in a few things but I decided to check up on you before hoof," said The Doctor in a cheerful manner.

"That is Princess Twilight Sparkle to you, Doctor Whooves. And I don't need checking up on!"

"It's just the Doctor if you please Twilight, and you do look like a mare who needs checking up on. I can see an uncertainty, and a loneliness in your eyes..." the Doctor's cheerful attitude morphing into a serious one.

"I... have no idea what you are talking about Doctor, now if you'll excuse me I'm trying to read!"

"Oh right, sorry! Daring Doo and The Castle of Doom, good one that," stated the Doctor. "But just remember this, I know you desire friendship, and friendship just may come from the most unexpected place if you would just give it a chance."

With that the Doctor quietly left the room closing the Door behind him, leaving behind a more than slightly confused Twilight. She had a feeling she would have to keep a close eye on that stallion.

She then promptly went back to reading her book.

Author's Notes:

So this is a slight filler chapter to shed some light on Twilights backstory in the altered timeline, back to our usual program next time!

4 - Making Friends

The Doctor walked into the console room of the TARDIS the gears in his head back at work. He knew the TARDIS scanners had to have picked up the unique temporal signature of whatever damaged the timeline in such a big way, the hard part however would be trying to isolate that signature among everything else.

The Doctor brought round the consoles monitor and began to sift through all the data the time machine collected when being struck by the anomaly, but there was a slight problem.

"Data corrupted?" the Doctor stared at the screen in disbelief, "Oh come on old girl you're better than this!"

The TARDIS gave out a low hum in protest.

"Well yes I know that you took a bit of a beating but this is important!"

A beeping noise came from the console

"Oh fine then, no need for that sass!"

The Doctor sighed, it would take days to make the data into something usable, this was going to be a tedious week.

The following morning the five element bearers sat in the royal dining room waiting for Twilight to come down for breakfast.

"So what's the plan guys?" asked Rainbow Dash

"No plan, we just act like ourselves and show her a little kindness!" said Fluttershy in a rare bout of confidence.

"Maybe we can throw her that party I wanted!" shouted Pinkie Pie

"Pinkie, maybe we should save that until we know she isn't going to turn us into ash," deadpanned Rainbow

"Honestly I agree with Rainbow darling, Fluttershy's idea should work but a party might just overwhelm somepony of her... volatile nature..." Rarity nodded agreeingly to Rainbow.

"Hold on y'all here she comes," whispered Applejack

A moment later the dining room doors opened with a push from a purple magical aura. Sure enough in walked Princess Twilight Sparkle, her evil green eyes seemed to glow brighter in the morning sun complemented by the fact she showed absolutely no emotion on her face. The five bearers watched as Twilight sat at the other end of the table and examined the food placed out on the table.

Applejack could of sworn that Twilight's eyes lit up for a moment as she laid eyes on the pancakes piled on the table before they returned to their emotionless black expression.

"Like ya pancakes, sugarcube?" asked Applejack in a friendly manner as Twilight picked up several blueberry pancakes and put them on her plate.

"I beg your pardon?" she responded coldly

"I saw your eyes glint for a moment when you saw those there pancakes, I'm sure the chef's would be delighted you enjoy them so!" an unfazed Applejack responded to the dark alicorn.

"I have no idea what your talking about," she lied

Applejack chuckled. "No point lying ta me bout such a simple thing sugarcube, as the Element of Honesty I can pick up such lies a mile away," she proclaimed proudly.

Twilight sighed. "Good for you" she deadpanned. "If you must know, my mother used to make blueberry pancakes for me when I was younger, and still does on occasion. As such they have become my favourite breakfast to have in the morning."

The Element Bearers all made a mental note of this as they moved over to join Twilight at her end of the table, much to her annoyance.

"My names Applejack, and them there are Rainbow Dash, Fluttershy, Pinkie Pie and Rarity."

Twilight raised an eyebrow as she examined the five smiling ponies.

"You're the Element Bearers, Celestia's 'elite' guard. What's your story anyways?" asked a genuinely curious Twilight.

Rarity was the one to answer this time. "Well you see darling I used to own a boutique in Ponyville, but when it came to light I was the Element of Generosity I joined this merry band without a second thought! Oh and if you ever need a dress fixing up for whatever occasion I can make you one on the house!"

Now it was Pinkie's turn, and much to Twilights surprise she almost seemed to teleport from her seat and appeared face-to-face with the alicorn.

"HiImPinkieAndIAmASuperDuperPartyPonyIAmAlsoTheElementOfLaughterWhichIsAwesomeBecauseILoveToMakePoniesLaughAndILoveMeetingNewPoniesBecauseIAlwaysMakeThemMyFriendsSoWouldYouLikeToBeMyFriendTwilightOfCourseYouWouldYAY!" Pinkie inhaled deeply and then exhaled before giving Twilight a squee.

Twilight just stared at the pink pony a few seconds before asking. "Is she always like this?"

"Yup!" Pinkie shouted before hopping back to her seat.

"OK... and you?" Twilight asked Applejack as she took a bite of her pancakes.

"Me? Well I ain't much to talk about sugarcube. Worked on my family farm, Sweet Apple Acres, before coming here. My big brother, Big Macintosh, is currently running the farm in my stead; the only downside to being a bearer is that I only tend to see my family at the reunions, but I have a duty and by Celestia ah intend to do it!"

"Uh huh, and her?" Twilight pointed at the Fluttershy, who's confidence seemed to dissolve as Twilight directly confronted her.

"I... uh... I'm Flutteshy..."

"Yes I know your name, what's your history?"

"Well I... er... well..." Fluttershy gulped. "I'm the Element of Kindness because I like looking after animals..."

"You like animals, that's it?"

Fluttershy nodded, obviously wanting to move on from the conversation.

Twilight sighed in annoyance. "And what about you Rainbow Dash, you have a confident look to you, what's your story?"

Dash huffed at the dark alicorn. "Yeah wouldn't you like to know, 'Princess'."

Applejack facehoofed. "Oh for the love of... Rainbow here was pointed to joinin' the Wonderbolts, but when it was revealed she was the Element of Loyalty she gave up on her dream and joined us instead. She's also slow to trust as you may of seen." Applejack glared at Rainbow who just shrugged.

Twilight looked between the five ponies, but couldn't help but notice something missing. "Hey, where is the Element of Magic?"

Applejack shook her head. "Sadly, we haven't truly found him or her yet," she said half truthfully while not making eye contact with the dark alicorn who, thanks to the Doctor, they now knew WAS the future bearer Element of Magic. In another life at the very least.

Rainbow dash became visibly annoyed. "Yeah just tell the enemy all our disadvantages why don't you!" Rainbow pointed a hoof accusingly at Applejack.

"Simmer down there sally! How do we expect to befriend her if we lie to her?" argued Applejack staring down Rainbow Dash

Twilight almost spit out her bite of pancake. "Wait! Befriend?"

Pinkie Pie was the one to respond. "Well yeah silly, otherwise I couldn't throw you an awesome party!"

Twilight pushed her plate away and began to leave the room. "Sorry but I don't have time for 'friends', now if you will excuse me..."

The Element Bearers looked between each other as Twilight left the room, but quickly got up to follow her.

Twilight sat in her room continuing to read her book from where she left off the previous day. All of a sudden a knock sounded from the door and Twilight reluctantly put her book down on the bed and got up to answer it.

When she opened the door she was met with the five element bearers looking at her rather sheepishly.

"What do you want? I'm trying to read!" Twilight asked rolling her eyes.

Applejack spoke up for the group. "Listen Twilight, ah know you're not in the business of making friends but..."

Before Applejack could finish a rainbow streak rushed past into the room, Rainbow Dash just hovered above the bed staring in awe at the book that lay on it

"Is that a signed edition of Daring Do and The Castle of Doom!?" she asked, trying not to fangirl.

Twilight walked up to the multi-coloured pony, perplexed by her reaction. "Why yes, it was a gift for my tenth birthday, two months before it even came out to the public..."

Rainbow let out a delighted squee. "Oh my gosh you are so lucky! Ever since Cadance introduced me to the series I've been trying so hard to get every signed edition possible, this is one of the only two I'm missing!"

"Wait!" Twilight shouted. "You've got signed edition of all but two Daring Do books?"

"Yep!" proclaimed a very proud Rainbow Dash.

Twilight gasped. "You have got to show me your collection!"

Soon enough the two mares got into a conversation about the book series they both seemed to love so much, the other four mares just stood there not understanding a single word they were saying.

"This may be easier than we thought," observed a rather amused Applejack.

After four days it was done! The Doctor had finally decompiled the data into something usable and was now looking through it to find out who Sombra's mysterious benefactor was.

"Nope, nope, nope... Ah ha!" shouted The Doctor triumphantly as a unique signature appeared on the screen before him.

"I've got you now, I'll just focus in, clear up the scan and..." the Doctor's smile faded as the unique temporal signature was displayed in full on the monitor, he had seen this signature before.

"That's not possible..."

Over the last four days Twilight had been spending a lot of time with the element bearers who had noticed Twilight had been coming more and more out of her shell as time went along.

Twilight remembered that party Pinkie had thrown on the second day, she had baked the most amazing blueberry muffins Twilight had ever
tasted and Twilight had genuinely enjoyed herself. Celestia herself had even briefly attended during which time she and Twilight got talking about the politics of their respective countries and how tiresome it was.

Now on the fourth day she sat in her room talking with her apparent 'friends', but calling them that still didn't seem right, what if this was all a trick? What if them befriending her was all a ruse to get her to reveal her empires secrets?

"You know that's that case," said a voice in her head

Twilight looked around. "Huh? Who's there?"

"What was that darling?" asked Rarity

"What? Oh, nothing..."

"They are using you Twilight, you have a duty, kill Celestia!" the voice commanded

"They wouldn't use me for their own benefit... would they?" she whispered to herself

"Of course they would, as your father's benefactor it's my job to know these things..."

Twilights eyes widened. "You? Then... what should I do?"

"Kick them out, make them leave you alone and while they are getting over their probable confusion you strike Celestia down! Do your parents proud..."

Anger overtook Twilight, those mares had used her, she no longer wanted anything to do with them.

"Out," Twilight muttered angrily

The five mares stopped talking and all looked round at Twilight

"Pardon Twi?" Applejack said surprised at Twilight's sudden change in attitude

"I... said... GET OUT!" Screamed Twilight in a violent manner, terrifying the five unsuspecting mares.

What the five didn't notice as they scurried out the room was a single tear fall down the lavender mares cheek as she watched them leave.

The Doctor walked out of the TARDIS quietly, a dark shadow formed behind him and an old enemy emerged from it.

"It was you... you caused this... you're Sombra's benefactor!"

The Doctor looked at the figure, he was a cloaked bi-pedal being, the only part of his body that was visible in his dark as night cloak was his grotesque face, on which sat only a mouth filled with razor sharp teeth. His skin was wrinkled and cracked and where his eyes should be only sat empty sockets covered with yet more cracked and wrinkled skin.

The figure addressed The Doctor, "Your explosive departure from our own universe provided me with an opportunity Doctor, one I could not ignore."

The Doctor looked upon the figure in disgust, the chaos bringer, a being who changed the timeline to a more horrific state and then fed off the chaos that followed, a creature the Doctor had fought several times in the past but an old companion of his had fought more.

"Trickster."

Author's Notes:

Rather calm subdued chapter this time, the calm before storm!

Next time things are going down to china town!
(Remind me never to say that again)

5 - Assassination

"Tell me Doctor, did you really think your presence here would be without consequence? Where you go chaos always follows," taunted The Trickster.

"I know, but I am here, and I'm going to stop you!"

"Stop me? You seem confident Doctor."

"You failed at Sarah Jane's wedding, you failed when faced with Donna Noble, and you will fail again!"

"Ah, Sarah Jane Smith and Donna Noble, both former companions of yours if I recall, but the thing is Doctor, where are your Companions now? Derpy is off who knows where, the Element Bearers barely know you and Twilight Sparkle..." The Trickster gave a sinister chuckle. "She is most important to me, the chaos she is about to unleash will feed me for a long time..."

"Look, just tell me one thing, how?" asked The Doctor

"I arrived in this universe about a thousand years ago, and while there I discovered Sombra, imprisoned. We made a deal, I would release him and bring back the Crystal Empire in return for him doing as I say when I say it."

"And he agreed?"

"I showed him there are... consequences for disappointing me. After I got Sombra I discovered poor Princess Luna, she was so alone and on the verge of such darkness, I simply sped up that darkness and helped forge an alliance between her and Sombra. More recently I discovered Twilight Sparkle, I know how much of a threat the Element of Magic would be to my cause, so I turned her into an asset instead."

"She may have had a different upbringing, but under all that dark magic the Twilight I know still exists, and I won't let you manipulate her further!"

"Are you so sure, Doctor?"

A violent explosion sounded throughout the castle coming from the throne room.

"Celestia dies this day Doctor, and the fall of Equestria shall begin," stated The Trickster, fading away moments later.

"Twilight..." muttered The Doctor before bolting off in the direction of the throne room.

Twilight sat in her room going through the weeks events in her mind, her thoughts specifically going to The Doctors words. "I know you desire friendship, and friendship just may come from the most unexpected place if you would just give it a chance."

Those five mares had offered their friendship, tried everything to make her comfortable in her stay at the castle, and it had been working until she kicked them out.

'Was I too brash, should I have given them a chance?' Twilight thought to herself.

Twilight shook her head to rid herself of these thoughts. The week was coming to an end and it was now or never, this day would be the last for Princess Celestia.

Twilight sighed, she wasn't sure if this was the right thing to do anymore, but she had a duty to her empire, and she was determined to see it through.

Twilight got up off her bed and walked out into the hallway, by this time Celestia should be muzzle deep in paperwork, a perfect time for a surprise attack. Twilight walked through the castle halls, concentrating on all the dark thoughts she could to build up the dark magical energy within her. Twilight soon came to the throne room and using the shadows to mask her presence quietly slipped in, Celestia sat on her throne sifting through piles of reports and forms, her concentration completely focused on them.

Twilight used her magic to cast some enchantments around the room, specifically a powerful magical field that would prevent anypony from entering, or leaving.

Still sticking to the shadows the dark alicorn crept up to where she had the clearest shot of Celestia and then called on all her gathered strength charging up an attack of dark energy, she stood there for a few seconds letting the reality of what she was about to do sweep over her.

And then she fired.

A magnificent explosion rocketed throughout the throne room as Celestia was launched violently from her throne straight into the wall, if it wasn't for Twilight's enchantment she probably would have gone right through it too.

A heavily bruised Celestia slowly looked up as she recovered from her daze, she saw that her throne and the paperwork she had spent the past three hours preparing was naught but ash. As the smoke cleared she saw a figure emerge from the haze, it was Twilight, her dark magic infused eyes glowing brighter than ever as a sadistic, evil look fell upon her face. Her horn glowed brightly as she unleashed another attack, this time Celestia managed to cast a shield around herself to block it, barely.

"Why, Twilight? All we have done since you arrived was offer our friendship!" proclaimed a saddened Celestia.

"Friendship? Overrated. Besides, I have a duty and I will fulfill it!"

"And to think they all believed in you," stated Celestia calmly as she got to her hooves, not hiding the disappointment in her voice.

That made Twilight hesitate momentarily, an opportunity Celestia didn't waste.

Celestia gave a flap of her wings and took to the air, lighting up her horn and using her magic to cast a devastating beam of golden magic towards the dark alicorn.

Twilight snapped out of her hesitation and narrowly avoided the blast, only getting slightly grazed by it.

The two alicorns began to fight, both blasting away at each other neither holding back, kicking and biting when they got the opportunity. Pillars crumpled when they got hit and priceless tapestries hundreds of years old were annihilated in fell swoops. Normally Celestia would be able to overpower Twilight fairly easily albeit after some effort, however Twilight's initial attack that caught Celestia off guard had done what it was intended to do and had physically crippled the alicorn for the remainder of the fight, they were now fighting on equal levels and the outcome was anypony's guess. All the while the Trickster looked on, confident his victory over the Doctor was nearly complete.

The element bearers sat in Cadance's room speaking with the Princess of Love, specifically discussing what went wrong with them trying to befriend Twilight.

"I don't understand it, the darling was really starting to come out of her shell for a while but then all of a sudden she didn't want anything to do with us anymore," said Rarity with concern in her voice.

"I'm sure she's just having a hard time, she's been raised to believe we are the enemy after all, now we are offering friendship she's going to be a little conflicted," responded Cadance, trying to ease the concerns of the five mares.

"Cadance may be right, she looked really, really sad when she threw us out and in turn that makes me really, really sad and..." Pinkie was suddenly cut of as she started to shake violently before suddenly stopping. "Huh, that one was a doozie."

"Your weird Pinkie sense right?" asked Rainbow.

"Yep, whatever it is its going to be massive!" proclaimed Pinkie.

Before the conversation could continue they all jumped as a loud explosion echoed throughout the whole castle.

Applejack frantically looked around. "What in tarnation!" she shouted.

"I think it came from the throne room!" squeaked a panicked Fluttershy

"You five go check it, I'll round up the guards and clear all servants and civilians from the area!" shouted Cadance pointing a hoof at the door.

"You got it Princess! Said Rainbow Dash putting on her helmet. "Let's go girls!"

With that the five mares ran out of the room and bolted towards the throne room. They passed several Solar Guards trying to clear the corridors of all non-essential personnel and a few others that saluted the five as they passed.

The Doctor was getting closer to the throne room, close enough to hear the battle raging within confirming his worst fears, Princess Twilight was attempting to assassinate Princess Celestia.

"Come on equine legs don't fail me now, Allons-y!" he shouted out loud to himself picking up the pace.

All of a sudden he ran right into the element bearers who were also running towards the throne room.

"Doctor!" shouted Rarity, "Do you have any clue what's going on!".

"Twilight's attacking Celestia!"

"WHAT!" the five shouted in unison, Fluttershy's voice being lost under the other fours'.

"No time to explain in full except that all this, the timeline changing as well as Twilight's current 'nature', it was all the Trickster he's been manipulating things since he arrived in the past!"

"Hold on there sugarcube, who the hay is 'Trickster'?" questioned Applejack.

"No time, we have to stop Twilight before she goes too far, right now she's still redeemable but once she's killed Celestia she will be lost to the darkness forever!" informed the Doctor, who was running off towards the throne room again followed closely by the five bearers.

Arriving at the throne room they could clearly hear the battle within, it did not sound pretty. Applejack got on her fore legs and tried to buck the throne room door open but was instead met with a magical field that deflected her and knocked her onto the hard floor.

"Ah, she's put up a magical field to keep anypony from getting in, and Celestia from getting out..." the Doctor muttered to himself.
Rainbow, having heard his mutter looked at him sternly. "Well then Doc? How do we get in?! We can hardly leave Celestia hanging!"

The Doctor turned and looked Dash straight in the eyes. "One, never ever call me Doc, it's Doctor". He then turned back to the door, picking up the sonic screwdriver as he said, "Two, magical fields work on a similar principal to more scientific forcefields, if I can find the right frequency with the sonic I can disperse it, it's easy really!"

The Doctor extended the sonic and a bright green glowed from the tip as a soft buzz sound was emitted from the device, the Doctor slowly moved the sonic around the door getting a clear scan of the field that surrounded it.

"May take a minute though!"

Applejack sighed, walked up to the door and shouted in. "Hold on Princess, we'll be in there in but a sec and y'all be right as rain ya hear me!"

Celestia destroyed a piece of broken pillar that Twilight had thrown towards the princess, pieces of stone dust rained down on her as she turned to face the dark princess of the crystal empire. Both mares were battered and exhausted, the fight was coming close to a close. Both sat hovering in place staring at each other, Celestia just above the debris that was once her throne and Twilight at the other end just in front of the door.

"You put up a good fight Celestia, but it won't matter! I will complete the task set for me!"

Both alicorns moved a little closer to each other.

"Listen to yourself! I know that underneath all that dark magic lies a good mare, a mare in need of our help, all you need to do is let us!" Celestia pleaded in vain.

"You waste your last breaths princess," sneered Twilight.

"Twilight Sparkle! I know Captain Shining Armor's little sister is still in there somewhere, please just listen to me!"

"Shining Armor, who the hay is Shining Armor?" asked a confused Twilight.

"I assume you are aware of where you came form, how you were stolen, taken from a loving family seeing you for the first time!"

"I... Sh... SHUT UP!" projected Twilight, who picked up another piece of debris in a purple aura and launched it towards the Princess of the Sun.

Celestia destroyed this piece also, giving out a sad sigh as Twilight's rage only grew. All exhaustion seemed to disappear from Celestia as her body grew calm and regal once more.

"I'm sorry it came to this, I truly, truly am," said Celestia calmly looking Twilight in the eyes.

Celestia's eyes weren't filled with anger or hate, not even disappointment. Instead they were filled with something else, pity, pity for a mare she had failed to save.

A muffled voice came from outside the throne room door. "Hold on Princess, we'll be in there in but a sec and y'all be right as rain ya hear me!"

"Huh, it appears your allies are here to save the princess, it's time to finish this now then..." snarled an enraged Twilight, who began to charge her horn once more.

"Twilight... they aren't my allies... they're my friends. As they are also yours," Celestia responded still using a calm demeanor, she too beginning to charge her horn.

Both mares charged their horns for a few more seconds, Twilight's aura a purple mixed with the black of dark magic, Celestia's was a bright, hopeful golden.

Once they were both fully charged both hovered there, observing one another for a second longer, neither noticing the throne room doors open.

Then they both fired.

The screwdriver's buzzing continued, the calculation 95% complete.

"Why are they not fighting anymore guys?" asked Pinkie Pie.

"What are they talking about do you think?" asked Rarity.

"Maybe they made up?" suggested a hopeful Fluttershy.

"Yeah, more like a brief pause before it starts again," deadpanned Rainbow Dash.

"Ah' sadly agree with Rainbow..." sighed Applejack.

The muffled conversation of the two alicorns within stopped and all became silent except for the sonic screwdriver.

"Ah! Calculation complete! The fields down lets get in there!" shouted The Doctor in victory.

The five Ponies and the Time Lord pushed on the door and it opened with ease, only for them to be met with a sudden explosion of magical energy as a purple/black beam collided a brilliant golden beam. All six where knocked right out of the throne room again by the shockwave.

Everything went dark

When the Doctor came round he looked up to see five ponies slumped on the floor. Slowly the Doctor got up and went to check on the five friends. To his relief all of them were OK, the explosion had just knocked the wind out of them.

An eerie silence crept over the six as they looked over at the throne room door, the door itself was charred and hanging off its hinges.

The six slowly walked forwards into the room itself, a twisted sight awaited them.

The throne room was in pieces, most of the roof was gone, unveiling the bright blue sky above. The walls were riddled with holes like a changelings hooves and all of the windows, pillars and tapestries were no more. Not even the throne itself survived.

The six pairs of eyes all fell onto the same thing however, in the middle of the room on the burnt remains of the red carpet that had once led to the throne lay two slumped, unmoving figures.

Celestia and Twilight.

From here the Doctor could see both were banged up pretty badly, cuts, bruises and burns all over their bodies. The six stood there for what seemed like hours, just staring at the scene before them. For the element bearers they had never seen destruction of this magnitude before, for the Doctor this was an eerie reminder of times gone past, the Last Great Time War coming to mind.

Celestia slowly opened her eyes and looked up at the days sky, breathing slow deep breaths, slowly she then clambered to her hooves, obviously in pain.

"Princess Celestia!" Exclaimed the Element Bearers, relieved to see the solar diarch on her four legs.

"Twilight?" Celestia asked, her eyes moving from the six figures to the one slumped on the floor.

The Doctor slowly approached the dark alicorn, coming to a stop next to her and bringing his ear down on her chest, listening for a heartbeat.

"Twilight..." whispered Fluttershy, beginning to sob.

"Why'd ya do it sugarcube?" whispered Applejack, slipping off the stetson she wore in place of a helmet and holding it to her chest.

"Doctor? Is... is she dead?" asked Celestia softly, despite everything she still didn't want Twilight to die.

The Doctor lifted up his head, a stern look on his face.

Location: Crystal Empire
Time Frame: 1785th year of Celestia's reign

King Sombra sat on the balcony on the crystal palace, watching sadistically as the crystal ponies below slaved away under the watchful eye of his guard.

A dark, cloaked bi-pedal figure appeared next to him as if from thin air, he looked out on the empire with Sombra.

"Greetings Trickster," said Sombra with no emotion in his voice.

"King Sombra, I am afraid Twilight Sparkle had failed, Celestia yet lives," informed The Trickster

"As I thought she would, Nightmare Moon wasted her time with that pitiful mare."

Trickster turned to look at the unicorn king. "Since the more subtle approach has failed, it's time to turn to a more direct approach instead."

"The army will be ready before the dawn, we march for Canterlot first thing," Sombra said, turning to face The Trickster.

"Good, do not fail me King Sombra, you know what happens to beings who don't keep their end of my deals".

"I understand," Sombra said, fully knowing the consequence of failure.

With that the Trickster disappeared, leaving Sombra to prepare for war.

Author's Notes:

Told you things were going down this time around...

6 - Week's End

The sun slowly began to rise as Celestia's horn glowed with that familiar golden glow of magical aura. With dawn now in place Celestia let out an exhausted drawn out sigh. Yesterday's events still played heavily on her mind.

However, despite Celestia's exhausted state she still had a duty to perform and she would see it through, but she couldn't help but worry what would happen in two days time when Sombra and Nightmare Moon would supposedly come to collect their daughter, and she was even more worried at how they would react to Celestia's survival.

Celestia looked out into the distance roughly in the direction of the distant Crystal Empire, "Oh Lulu" She muttered sadly, "Why do we have to fight as we do sister?"

Of course Celestia now knew why they fought, she now knew of the one who was truly behind all this. This Trickster character had changed all their destinies just to feed off the resulting chaos, this sounded familiar and her thoughts went to a certain statue which still sat in the Canterlot castle gardens.

"Yes your Discord and The Trickster would get on well I believe," Said a voice behind Celestia as if reading her mind.

Celestia turned around to find a familiar brown coated stallion with an hour glass cutie mark.

"Doctor, how are you this morning?"

"Oh I'm fine, it's you I'm worried about..."

Celestia smiled warmly. "I'll be fine in time, my little pony."

"Yes well 'time' is certainly the object here isn't it!" the Doctor chuckled before turning onto a more serious tone. "She's awake".

"Twilight?" Celestia gasped, that filly sure was resilient. "How is she?"

"Confused, she expected to be dead, the other five are already waiting for you." The Doctor looked Celestia dead in the eyes. "Celestia, you know she was manipulated since birth; there is still a light in her so just please, give her another chance..."

"I will do what's necessary, Doctor."

The Doctor sighed, but nodded in acceptance. He just hoped she would make the right choice.

Twilight lay in her bed, several medical apparatus sat throughout the room, Twilight had to wonder why they had done so much to save her life, if she had tried to kill her father she would already be dead, or at least undergoing unbearable torture in the dungeons.

Twilight sighed, her father never really cared for her, it was her mother that raised her. Oh how Twilight longed for her embrace, she would give anything to see her again, one last time before the punishment she was sure was still coming was inflicted upon her.

A clicking noise caught Twilight attention as the door to her room swung open and in came seven ponies. The Element Bearers looked unsure, Pinkie Pie's mane was also drooped instead of being in its usual cotton candy like configuration, the Doctor had a look of concern on his face and he was looking between Celestia and Twilight in apprehension. Celestia looked as regal as ever, but Twilight knew she was hiding the exhaustion she was feeling behind her usual mask. She looked down at Twilight with largely emotionless, but slightly judgmental eyes.

Twilight sighed. "My punishment has been decided I presume?"

Applejack stepped forward to address Twilight. "Why'd ya do it sugarcube? All we've done since y'all got here was try an' befriend ya."

"I have a duty to my empire, a duty I sadly failed. Anyway, I have it on good measure that your attempts to befriending me were nothing more than a trick."

"The Trickster," the Doctor proclaimed walking up to the bed.

"Excuse me?" Twilight asked in confusion.

"He's your fathers benefactor, he told you that your friendship was a lie, didn't he?"

Against her better judgement Twilight confirmed with a simple. "Yes."

The Doctor sighed. "Twilight, the Trickster has been manipulating you since you were born! To him you are a tool to cause unparalleled chaos, and he lied to you to keep you from rejecting his manipulations!"

Twilight didn't want to believe him, but something about those age old eyes told her he was telling the truth.

"So?" she asked. "What happens now?"

It was at this moment Rainbow Dash piped up. "I say we give her a second chance!"

All the ponies turned to face Rainbow surprised by her sudden outburst.

"Why do you say that Darling? She tried to kill the Princess!" exclaimed Rarity.

"I don't care! The poor egghead was taken from her birth parents and thrust into a life that wasn't meant to be hers, they've manipulated her since day one and now he knows the truth what kind of friends would we be if we abandoned her now?!"

Rainbow's four friends glanced between each other before nodding, all voicing their agreement with Rainbow Dash.

"Wait," Twilight muttered just audibly. "You really consider me a friend? It really wasn't a lie?"

Before Twilight knew it, the five Element Bearers had tacked Twilight in a group hug with Pinkie saying as her mane re-inflated. "Of course we do, silly! Why else would I throw you that epic party!".

Tears began to fill Twilight's eyes, but for the first time in a very long time they were tears of joy, not sadness.

"See, Celestia!" exclaimed The Doctor. "Even now the friendship those six have conquers all!"

Celestia chuckled. "Well then its certainly a good thing I was going to give her a second chance anyway!"

Celestia approached Twilight and the five Element Bearers ceased their group hug and parted to let her through.

"Besides, adopted or not I would certainly like to get to know my niece better," Celestia gave Twilight a warm, loving smile.

"I would like that," Twilight smiled back, nodding slightly in agreement

"Just one thing however..."

"Yes Celestia?"

"No more assassination attempts if you would be so kind."

Twilight chuckled. "I think I can accept those terms."

Two days later...

A large army consisting of both Crystal Pony's and various beasts and monstrosities marched onwards towards the city of Canterlot in the dead of night, the city had just been put on high alert and Sombra and Nightmare Moon stood on an outcropping overlooking their battle ready army.

"If Celestia has hurt Twilight..." Nightmare Moon muttered angrily.

"Then go on ahead of me, if she is alive she may be of use to us yet," Sombra told her with little emotion

"Use to us?" Nightmare Moon repeated. "She's our daughter, not a tool!"

Sombra didn't answer, instead he continued to look down on his army.

Nightmare Moon glared at him for a few moments before turning and taking to the skies, flying directly towards Canterlot castle.

Solar Guards ran about the castle evacuating all civilian personal as Twilight ran as fast as she could to the throne room, which was still undergoing repairs.

Twilight burst through the doors to find her five friends, Celestia and the Doctor already there.

"What's happening?!" shouted Twilight in a small panic.

"Your so called father, that's what!" exclaimed the Doctor. "According to Celestia's scouts, they marched all the way across Equestria under the cover of a powerful illusion spell. They are already too close for a shield to be placed around the city!"

"Twilight, can you talk to them? Make them stop their attack?" asked Celestia

The whole castle shook violently as it took a hit from a siege weapon.

"I may be able to convince mother, but father I highly doubt. He's never really held me in that high regard!"

"If only we had the Element of Magic, then we could possibly have used the elements to pacify the army!" proclaimed Rarity in exasperation.

The Doctor turned to Celestia. "Yes where is the Element of Magic itself located anyway? I mean those five have theirs embedded in their armour but I haven't seen that one anywhere!"

Celestia shook her head. "I do not know, that element disappeared almost a thousand years ago..."

"It's always a thousand years, isn't it..." the Doctor deadpanned.

Suddenly an almighty bang caught all of their attention as Nightmare Moon barreled into the throne room.

"Celetia! Where is my daughter?!" Nightmare Moon shouted as both a question and a challenge, before her eyes rested on a perfectly fine Twilight Sparkle.

"Mother!" shouted Twilight happily running up to the dark alicorn and embracing her.

"Oh my little star, I thought for sure I wouldn't see you again!"

Twilight broke away from the embrace and looked up at Nightmare Moon. "Yeah, we're luckily that lot gave me a second chance and nursed me back to health DESPITE me trying to kill Celestia," Twilight pointed a hoof towards the other ponies in the room who were all shuffling awkwardly.

"They... did?" Nightmare Moon asked, very surprised by this revelation.

"Luna," Celestia addressed her little sister as she slowly approached. "We don't have to fight anymore, we can be a family again! By this point that is all I want..."

"You can trust her, Mother!" Twilight confidently proclaimed. "I don't want this war anymore, and neither should you!"

Nightmare Moon looked between her daughter and her sister, unsure of what to do. She had been fighting her sister for so long, but she couldn't deny that she had missed Celestia and the relationship they once had.

Before Nightmare Moon could respond a voice echoed throughout the throne room. "My my Twilight, how very disappointing. This is how you repay me for bringing you into life of royalty?"

"Sombra," muttered The Doctor

Sure enough the evil king walked into the throne room. "Sorry about your guards Celestia, but they got in my way..."

"Father!" shouted Twilight running to put herself between Sombra and Celestia.

"Hardly," deadpanned Sombra. "But it doesn't matter, your real father will be dead before the night is over, as you will if you don't get out of the way."

"Sombra, you will not harm her! Do you understand?!" shouted Nightmare Moon

Sombra ignored her and continued to glare at Twilight.

"Twilight," Celestia addressed the young alicorn. "This is between me and Sombra, I don't want you getting hurt."

"No!" shouted Twilight in her seldom used Royal Canterlot Voice. "Sombra, it doesn't need to be like this! There is a chance for all of us to live side by side in peace and if there is one thing that my friends have taught me in the last few days..." Twilight briefly turned to view her friends before turning back to Sombra, "...is that friendship is magic! And it will overcome all!" Twilight stamped her hoof in conviction.

Time stood still for a moment as everypony fell silent, nopony spoke for what seemed like hours.

And then Sombra struck...

A huge beam of dark magic hit Twilight square in the chest and sent her flying out of the throne room and into the gardens outside.

"Twilight!" everypony but Sombra gave a terror filled shout.

"Nopony defies me!" shouted Sombra angrily as he followed Twilight out, intending to finish her off.

"No!" shouted Nightmare Moon who quickly followed Sombra outside.

"Well, it would appear Sombra is a bit more powerful in this timeline than the true one," observed The Doctor before hurriedly stating. "Well, come on you lot! We have to help Twilight!"

A mortally wounded Twilight lay in the Canterlot Gardens. Twilight's crown sat a few metres away having fallen from her head in the impact. Regaining her senses she attempted to stand up but found herself too weak to do so, she was not ready for combat so soon after her botched attempt to kill Celestia.

Looking up Twilight saw Sombra approaching, horn glowing with dark magic ready for the killing blow.

"It's a shame, Trickster saw so much promise in you, sadly it would seem you did not live up to that promise... goodbye Twilight," Sombra sneered.

Twilight closed her eyes, waiting for her end.

Author's Notes:

Cliffhanger! Again... I'm so sorry XD

7 - The Trickster and The Doctor

A mortally wounded Twilight lay in the Canterlot Gardens. Regaining her senses she attempted to stand up but found herself too weak to do so, she was not ready for combat so soon after her botched attempt to kill Celestia.

Looking up, Twilight saw Sombra approaching, horn glowing with dark magic ready for the killing blow.

"It's a shame, Trickster saw so much promise in you, sadly it would seem you did not live up to that promise... goodbye Twilight," Sombra sneered.

Twilight closed her eyes, waiting for her end as she heard Sombra fire the magical beam.

It didn't come.

Opening her eyes she was met with Nightmare Moon facing away from Twilight with a shield around her. She had saved Twilight!

King Sombra growled as his now former wife glared at him challengingly.

Nightmare Moon's eyes glowed a bright white as in her Royal Canterlot Voice she addressed the dark king. "Nopony... tries to kill... my... DAUGHTER!" With that her shield warped back into her horn and was then fired at Sombra as a powerful energy projectile, soon enough Sombra and Nightmare Moon were locked on a battle to the death.

"Twilight!" Twilight heard several voices cry out just before six pony's crowded around her, with one bright alabaster alicorn breezing past the group and joining her sister in the battle against Sombra.

With the battle raging in the background, the Doctor pulled out his sonic and began to scan Twilight as the mare grew paler.

The Doctor's expression turned to sorrow. "She's hurt, badly. I don't know what I can do in this case, I'm sorry."

Fluttershy looked down at the injured alicorn. "There there Twilight, we are here for you," she cooed, suppressing tears.

Applejack nodded in agreement,."You bet Twi! We are ya friends and we ain't goin' nowhere!"

Twilight weakly looked up at the group. "Honesty, Loyalty, Generosity, Kindness and Laughter, I couldn't have asked for better friends, I love you all!"

With that final declaration from Twilight the five elements began to glow and emit beams of light, these beams mixed just above Twilight and a lavender crystal in the shape of a star began to form.

"Don't forget, Twilight, the most elusive and powerful of the elements," The Doctor said his mood lifting significantly. "Your element, magic..."

When the elements where done on top of Twilight's head sat a golden crown with the Element of Magic embedded in the centre, all six
elements began to glow and Twilight's wounds seemed to heal themselves.

"No!" shouted Sombra who tried to fire a bolt of magic at the group, but was intercepted by Celestia.

The Doctor stood back as Twilight got to her hooves. "You ready girls?" she asked the group, who nodded in confirmation.

Before they used the elements on Sombra however, a shadow seemed to form in front of the group and a familiar bi-pedal monstrosity stepped out, the Trickster had arrived.

"Twilight Sparkle, how disappointing, but its not too late, I can make a deal with you. Join me and we shall kill all three of those combatants, and I can put you in charge of this entire empire, all that power yours to command as you see fit..."

Twilight stared at The Trickster for a few moments before giving her answer...

"No."

"What?" The Trickster was surprised by her rejection.

"No, that's not who I am anymore," she stated with conviction, the dark magic that had flowed from her eyes for so long finally dissipating
turning from them from a sickly green to a wonderful lavender that matched her coat.

The Doctor laughed in victory before directly addressing the Trickster.

"You were right about one thing Trickster! Every time I beat you in the past I had companions, friends, and here they are! That's how it should be and that's how it will always be! Because Trickster one thing you will never, ever, understand is that it is our friends, not your stupid deals and dark magic that gives us true power, power to face down the whole universe and any other universe that may exist! And that is why you will always lose!"

The Trickster snarled at the triumphant Doctor. "Well Doctor, let's see how you like losing your friends."

The Trickster outstretched one of his hands and from it great discharges of energy resembling lightning erupted, striking the Element Bearers who all shouted out in pain as their elements dulled slightly.

"Watch as they die Doctor! Watch their pain as they-" The Trickster didn't get the chance to finish his sentence as he was tackled to the ground by none other than the Doctor himself.

"I can't hold him for long, use the elements!" the Doctor shouted.

The six Element Bearers got to their hooves and looked to the Doctor with worry.

"What about you? You will be hit too!" shouted Twilight with great concern.

"I'll be fine!" the Doctor shouted as he struggled with The Trickster. "Just hurry up already!"

Twilight nodded and began to charge the element of magic, all the other element bearers followed suit quickly, the three combatants stopped their fighting and all turned to look at the scene before them.

"Oh horseapples," muttered Sombra in defeat.

The six mares levitated off the ground and Twilight eyes glowed a brilliant white as a rainbow coloured aura blasted out and struck both the Trickster and the Doctor head on.

In the distance you may have heard the TARDIS cloister bell sound as time began to reset with the defeat of the one who had changed it in the first place. The elements cleansed all his tampering and darkness, the restoration bringing back all that was lost.

The Doctor opened his eyes and was met with a bright blue sky, looking around her could see eight other ponies all collapsed on the ground of the garden but all were beginning to wake up. The Element Bearers were no longer wearing any armor and the elements were gone, being embedded in the tree of harmony in this timeline. Nightmare Moon was also gone and Princess Luna was in her place.

The group all got up and examined their surroundings in confusion, Rarity was the first to speak.

"Well, what are we all doing here? Were we not just in the castle examining the map?"

"No silly!" Pinkie spoke up. "Don't you remember the alternate timeline where Twilight was evil but then she wasn't and then we all became friends again and beat the bad guys!"

"I do," said Celestia. "But it's hazy, almost like a dream, will it be like this for all my little ponies, Doctor?"

"No of course not!" the Doctor exclaimed happily. "Just you lot because you were caught in the edge the element's blast. So for all of you it will be like a vivid dream! Well, except for Sombra that is because he's dead in this timeline but yes, it did all really happen."

Twilight and Luna approached each other rather sheepishly.

Luna looked at Twilight and asked. "In that timeline were you..."

"Your adopted daughter, yeah...."

"So does that mean..."

"I have no idea..."

Twilight and Luna just sat there awkwardly not knowing what to say, much to the amusement of Celestia.

Finally Twilight spoke. "You know what, Luna? For the record you were a great mother..." she said smiling at Luna, who smiled warmly back.

"Hey, what happened to the Trickster?" asked Twilight, turning her attention to the Doctor who was scanning the air with the sonic screwdriver.

"Well Twilight, only those at the centre of the blast carry on perfectly from the aborted timeline, which is me and The Trickster, who is alive but seems to have been disembodied permanently. I think we're breathing him right now..."

Rarity put her hoof to her mouth to stop herself from then throwing up before fainting onto a fainting couch so thoughtfully provided by Pinkie, who seemed to get it from thin air.

Twilight rolled her eyes at their antics before turning to the Doctor again, this time with concern in her eyes. "And what about you Doctor? Did you really escape the element's blast completely unharmed?"

"It seems that way!" the Doctor twirled his screwdriver before placing it back in its holster. "I've never felt better! In fact I would say that... that..."

The Doctor paused, a sudden realisation dawning over him.

"Oh no."

The Doctor doubled over in pain causing panic among the others present, who all ran to his aid. As the Doctor got up a small golden glow appeared to come from his body before vanishing. The others backed away to give The Doctor some space as he motioned with his hoof.

"No..." the Doctor muttered. "My usual reward then..."

The Doctor stamped his hoof in anger before shouting to nopony in particular. "One year! Is that all I get? One measly year before another has to take my place?!"

"Doctor? Is thou alright?"asked Luna

"The elements appear to have triggered my regeneration..."

"Regener-what-now?" asked a confused Applejack

"Regeneration, when a Time Lord dies we have a way of cheating death, we can only do it a certain amount of times but rather recently I got a new cycle, but the downside is it means I have to change."

Twilight's concern grew. "Change? In what way?"

"In every way," deadpanned the Doctor. "Well almost, I'm still the same man, or stallion in this case, so my core personality traits stay the same but my appearance and some of my 'outer personality traits' change..."

The Doctor sighed before quickly pulling out his screwdriver and summoned the repaired TARDIS which materialized with the ever so iconic wheezing sound.

"Where are you going?" Celestia inquired.

"I promised Derpy a journey in time and space and before I go that's what I intend to do! But don't worry, when the time comes I will return, it will be nice to have some friends at my side this time around."

The Doctor looked between them, smiling. "You know something, you were brilliant, all of you, fantastic even. It may have been just a year, but I will always remember this, every second of every day, I'll always remember when the Doctor was me..."

With that The Doctor jumped into the TARDIS without another word which dematerialized moments later, the blue box disappearing into the time vortex once more.

Later that day Twilight and Celestia just sat on a balcony overlooking Canterlot discussing recent events, events that no longer existed it would seem, but they knew that while they didn't exist, hey still happened, time travel is complicated like that.

"Well I'm just glad I didn't kill you Princess, sorry about that by the way..." Twilight shrunk down a little bit at the thought of that particular memory.

"As am I, but you have nothing to apologise for Twilight. It wasn't your fault but the fault of a monster that in a way was worse than Discord ever was," Celestia responded to Twilight's relief, before something else that had been bothering her came to the surface.

"It's not fair," muttered Twilight. "After all he did for us he has to die..."

"Fate is rarely kind, my most faithful student," Celestia sighed. "But I have a feeling while this chapter is ending for him, his story will not be ending anytime soon."

Author's Notes:

Just the epilogue left now, hope you enjoyed my first story!

8 - Epilogue

Location: Time Vortex
Time Frame: N/A

Derpy slept peacefully on the floor of the TARDIS, the Doctor observing her somewhat guiltily. He had been holding in his regeneration too long, it was becoming volatile, it exploded out and knocked Derpy unconscious, she was fine thankfully, but this incident had made the Doctor realise it was time.

"Derpy, before I go I want you to know you were brilliant, just completely brilliant," the Doctor said to the unconscious pony.

The Doctor approached the console in pain and put in the coordinates for his final destination, Canterlot Castle. He had promised to return when the time came and he intended to keep that promise, besides, he didn't want to die alone.

Location: Ponyville
Time Frame: 1785th year of Celestia's reign

Princess Twilight Sparkle sat quietly on her bedroom balcony, observing all of Ponyville high up from her castle. It had been two months since the Doctor regenerated and destroyed the Canterlot throne room in the process, rebuilding had only just finished! But in all those two months there had been no sign of the Doctor or Derpy.

Twilight had to wonder when and where the Doctor will appear again, when she see's them again will it be moments for them after the regeneration, or will it be...

As if on cue an unusually sickly sounding TARDIS materialization began to echo throughout the whole town, looking up Twilight just caught a glimpse of a familiar blue box crash landing right smack bang into the centre of Ponyville.

"Spike, send a letter to the princess! The Doctor has just shown up, and I think it has been mere minutes for him!"

With that Twilight took to the skies and flew towards the crater at the centre of town.

"Here we go again," Twilight said with a chuckle

Author's Notes:

So here we are! The end! For now at least, I'm not quite done with the Doctor just yet, spoilers ;)

The regeneration video was by SlyphStorm, and was the video that partially inspired me to do this story.

Until next time! Allons-y!