Prologue
A thousand years ago...
Celestia and Luna walked towards Discord, determination gleaming in their eyes. They were finally able to stop Discord and his chaotic reign once and for all. Discord on the other hand, was not paying any attention to them almost as if they didn't exist. The two sisters kept on walking towards Discord until he turned his throne around to face the Alicorns.
"Oh, this is so much fun! Who wants to play 'Pin the Tail on the Pony'?" Discord said as he held up Celestia's tail.
Surprised to see her tail in the draconequus's clutches, she turned her head around to find that her tail was missing.
"Playtime is over for you, Discord!" Celestia said sternly.
Discord simply replied "Oh, I doubt that," while munching on a seed from a bag that he conjured up with his magic.
"Hungry?" He then threw a seed each at the two sisters which they completely ignored. "Well, suit yourself."
Celestia had enough. Looking at Discord with an angry glare, she levitated the Elements of Harmony out of her saddlebag with her sister soon following. Then they activated the elements which only piqued his curiosity.
"Ooooh, what have you got there?"
Celestia replied "The Elements of Harmony!"
"With them we shall defeat you!" Luna promptly followed.
But even with that Discord was not intimidated. As Celestia and Luna were charging their attack against Discord, he started to laugh.
"You should see yourselves right now! The expressions on your face, so intense, so sure of yourselves!"
But the two sisters did not listen. The Elements of Harmony launched their attack on the still laughing Discord.
"But no matter what you do, you can't defeat me or my da--"
Discord didn't get to finish his last words as the Elements of Harmony blasted a huge rainbow beam raining down on him, turning Discord into stone. A beautiful rainbow wave restored harmony and erased his chaos.
When the Elements finally stopped, Celestia and Luna fell down onto to the grass that they were now on. The two were completely exhausted from using so much magic. Even with the Elements of Harmony, defeating Discord and reversing the damage he had done had taken a lot of energy out of the two sisters. After some time, Celestia and Luna got up and gaped at what they accomplished.
Luna was first to talk, "It seems that the Elements are stronger than we originally thought."
"Agreed," Celestia said.
The two smiled. The chaos was finally over. The ponies could go back to their normal lives without worrying whether there house would be flipped upside down today. All was good.
But then, they heard a whimper.
Looking around, trying to find where the sound had come from, Celestia found that the sound was coming from the stone statue that was Discord. When the two walked over to the statue they noticed a small creature hiding behind the statue. Celestia walked closer to the hiding creature. Celestia held her hoof out to the small creature and waited patiently for its response.
When the creature finally mustered up enough courage to interact with the stranger, the creature revealed itself to the sisters, but when the Alicorns saw the creature, they were astonished.
They were speechless to what they saw in front of them. As what they saw was a young draconequus.
The draconequus cub's body was mostly purple, with its neck and body fur being in different hues. The head was pony shaped but its ears were big and floppy and two small stubs protruded from behind its head. Its mane was messy and colored dark blue with stripes of magenta and lavender streaking through it. Its eyes were similar to Discord's, with a yellow sclera and no iris, but it had a violet pupil instead of red. Its forelegs were that of an eagle, colored in darker shade of purple than its body fur. Its hind legs were that of some big cat in the same shade of purple as its forelegs. It had hot pink serpent's tail with a tuft of hair, the same coloration as its mane, at the end of it. On its back were two small pegasus wings. Taking a closer look at the draconequus they were able to identify it as a female.
However Luna did not care for its looks but more for what it was.
"Sister we must vanquish this beast at once!" Luna shouted
"Now hold on, this draconequus is still very young," Celestia calmly replied "Although it may pose a threat to Equestria, I believe that she has no ill will against this world to do so."
"Sister we do not even know where she came from!" Luna shouted "For all we know it could be Discord's daughter!"
Then there was silence.
Could it be? Is this draconequus, Discord's daughter? Who's the mother? Would it be safe to spare her from the Elements of Harmony? Hundreds of questions ran through Celestia's mind.
"Sister?" Luna asked
Celestia snapped back to her senses
"Hmmm, maybe it is best we keep her hidden from the populace. At least until the ponies get settled back into their new lives" Celestia said
"Are you sure about this, Sister? I don't think the ponies here want to see another draconequus. They would have to forget about, Discord's reign if the draconequus wants to live out here. Even then it still poses a threat to Equestria. If we kept it in hiding, who knows what it'll try to do? It might even try to avenge its Father!"
"Luna, we don't know that yet. We don't even know if this draconequus is, Discord's daughter!"
"Then why don't we try that heritage spell we found in the Castle Library?" Luna said "Then, we can know for sure,"
Celestia pondered about this for a moment. 'That would clear up a few unanswered questions' Celestia thought.
"Do it then."
Luna lit her horn and began to cast the spell on the draconequus who now looked terrified. It was now flailing its limbs as it was being lifted up in the air. When the spell completed its task the draconequus was put back down, a display then came up above the its head and on it was Discord's name, a question mark, and one other name that read "Twilight Sparkle".
"Oh dear," Celestia said
"Well I believe that settles it then," Luna said in a rather cocky tone.
"Why is there a question mark next to, Discord's name?" Celestia asked
"I don't know,"
"Well then I guess this 'Twilight Sparkle' is the draconequus in front of us,"
"Now that's settled with, what should we do with her?"
"Well, we can't let the ponies here know about her," Celestia answered.
"I'm still wondering why you want to help her in the first place," Luna replied.
"You know it would be wrong to use the Elements of Harmony on an innocent,"
"She's Discord's daughter!" Luna shouted back.
"What does that have to do with anything!? She hasn't done anything wrong!"
Luna pondered on her sisters words. "Fine, I'll let her go."
Twilight was now quivering in fear behind the statue
"Maybe instead of just hiding her, we'll put her in a state of sleep and remove any memories of her life. At least until the ponies of this land forget about Discord's reign."
"Are you sure about this?" Luna replied. "Faust knows how long that could take. This 'Twilight' could grow up while in her sleep and when she wakes up most likely cause Chaos like her Father."
"Then we put her in a preservation crystal," Celestia said "Then she will stay as a child until she awakens."
"Sister..." Luna looked a bit hesitant about this plan "Are you sure about this?"
"Yes," Celestia replied
"Well, if you believe that is what's best for us, then I shall have no objections,"
Celestia lit her horn. Twilight was looking at the two curiously, wondering what was going on. She slowly backed away and was about to run away until Celestia's magic got hold of her and put her to sleep. She was then encased in a crystal twice as big as her. Her memories were buried deep in her brain.
"It has been done,"
So yeah, this is the first chapter I've ever written so expect a lot of mistakes. I would appreciate some criticism to help me improve my writing! 
Also draconequus Twilight is based of Lopoddity's (a.k.a best Twicord shipper)
Thank you to Zocarik for proofreading this chapter.
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I enjoyed this very much, I like the idea of her originally being a draconequus, as i've read a few stories where she turned herself into one. I feel like you should make the chapters longer, but that's all about personal preference. As I enjoy getting deep into the tale the story tells, yet some don't, the grammar and spelling issues are minimal, if any, as I didn't pay much attention to that. All-in-all it was great and I would love to see it continue.
I think its interesting and would really like more of this
In the last sentance there is a "know" that I think should be a "now"
no bigger mistakes... that i noticed.
hope to see more of this
Try not misspelling the very first word in the story.
Prologue.
....Hmm.
Interesting concept. Your flow is decent, though a little too fast--you're favoring action over contemplation, not giving the characters enough time to seriously consider before they say their next line. And there are the numerous grammar errors, but in my mind grammar is more 'maintaining the paintbrush' than actually 'painting' if that makes sense.
This could be fun to watch.
great idea, I look forward to this story
I like what you have so far hope to read more soon
I'm liking this so far. I'd like to see more.
Consider me intrigued.
Well, this is interesting and fairly well-written. I look forward to more.
Sorry for bugging you but do you know when you might be posting the next chapter
7199510 It's been a bit difficult writing the next chapter. I hope to release the next chapter by the end of the month.
7199849 oh its is okay I understand I wish you the best of luck with the next chapter
look over and wonder if the stories shall be continue
MOAR!!!
7199849 hey hows it going???
7313649 I'm going on vacation soon so I might not be able to work on the story for a while but I'll try to get it done. I've just been hitting a few writer's blocks that's all
7314096 oh too bad on the writer's blocks
but grate on going on vacation it might help you come up with some new idles. I hope you have a grate time.
7314096 does draconequus Twilight like this
pre15.deviantart.net/3040/th/pre/i/2015/014/b/e/magical_mystery_oops_by_lopoddity-d8dyec7.png
7354600 Yup
You got a strong start, let's see you roll with it
7314096 Hey how was your vacation did you have fun???
mmm just reread this chapter and so good, hmmmm will she remember everything or will she not remember......
Did you mean without?
I like where this is going.
A typo I found
I think you mean so much magic.
The concept is interesting, but it's a bit tough to read. It's very flat and stilted, and I found it easy to just skim.
I honestly would not be surprised if Twilight's mother's name was '?', especially assuming they're a draconequus.
They did not give any reason as to why they wiped the memories of an innocent child. No contemplation at all, just action. Makes it difficult to take their decision seriously.
7354600
AAAAAAAAAAAAAAAAHHHHHHHHHHHHHHHH!!!!!!!!!!!!!!
She too cute!