Prologue
The Wastelands.
A desolate place where poisonous sulfur dioxide gas kills all who enter; a place devoid of all life. The rain won't fall, the trees won't grow, not even a tumbleweed can be seen rolling through. Nothing but barren earth for as far as one can see.
Long, long ago, in the time before Nightmare Moon, the Wastelands used to be known as FlutterValley. The home of the peaceful Flutterponies. Too bad the peace didn't last.
The Flutterponies watched in horror as their home burned, helpless to do anything. They reached out to Celestia for help, but Celestia didn't answer, nopony did. It was on that day, as the remains of their home burned to ash, that a seed was planted within the hearts of the Flutterponies.
This seed corrupted them, mutated them, until the only part of them that even remotely resembled what they had once been was the delicate wings attached to their backs. And even their wings had been affected by the seed of corruption. It was upon that day that the Flutterponies took a new name, one that would strike fear into the hearts of foals for many a year to come.
Changelings.
They traversed the lands of Equestria, feeding off the love the ponies, wreaking their vengeance upon those that had abandoned them in their time of need. Then one day, led by Queen Chrysalis, their first and only queen, the Changelings flew back to the Wastelands, where they would hide underground for one thousand years, biding their time.
When the Changelings returned it was clear they had fallen on rough times. Not only was the army they came back with half the size it had been, but they looked half starved.
Needless to say they were beaten back, the Elements of Harmony protected Equestria, expelling the dying nation into the Everfree forest, and in doing so, placed the Changelings on the extinction list.Or so it was assumed.
For one Changeling survived, the strongest Changeling of them all, the one that still had a reason to live... Queen Chrysalis. Unfortunately for the queen of the Changelings, she could not just lay eggs and wait until it hatched, because it wouldn't. She needed another Changeling to fertilize the egg by giving it the love that she gave to them after she had collected it.
She was the last of her kind. Good thing she was immortal. Queen Chrysalis was pissed at the Equestrians... No, that's an understatement. She wanted to murder every last one of them. But she wouldn't do it even if she had that kind of power, she wasn't that kind of pony.
She hid within the Everfree forest, just outside Equestria's borders. They couldn't hold her prisoner even if they found her. Chrysalis had fallen as far as she possibly could, reduced to letting bats nest on her to obtain the love her species needed to survive. She was a truly pitiful sight.
The bats followed Chrysalis everywhere, swarming around her as they fought for a place on her black exoskeleton, and giving away her position at the same time. It made Chrysalis sick with disgust.
"The bats are this way, I can hear them fighting! Ohhh, I can't wait to tell the Princess all about it!"
Chrysalis froze in place, the bats calming down as they each found a spot, effectively hiding her from view.
She knew that voice, it was the voice of the Unicorn that ruined her plans, she internally pleaded to any and all gods for Twilight Sparkle to go away and leave her alone.Too bad Discord was the god that decided to answer.
Chrysalis could hear Twilight Sparkle walking in circles around her. Fear gripped her black heart mercilessly, and it had no intention of letting go.
"Why would bats nest in the shape of an Alicorn? Hmm..."
The sound of a quill writing on paper alerted Chrysalis to the fact that Twilight was taking notes. Chrysalis muttered a curse underneath her breath, her eyes widening when she realized that Twilight would no doubt hear her in the silence that surrounded this section of the forest.
Twilight's warm breath blew on the bats covering her face. They shifted slightly under the assault.
Chrysalis opened her eyes and mouth, using her magic to create a soft green light pouring out of them, hopefully giving off the illusion that she was a magic statue or something.
"GO AWAY." Chrysalis boomed stoically, making sure to magically disguise her voice on the off chance that Twilight recognized it. Discord must have been having a terrible day so far, because Twilight Sparkle did not leave, instead she just continued to take notes.
Chrysalis's patience began to grow thin. Raising a forehoof up off the ground slowly, so the bats could hang on, she took a step forward, using her magic to send a shockwave through the ground, making it seem to the casual observer that Chrysalis was much heavier than she actually was. Twilight Sparkle was smarter then that.
"GO AWAY." Chrysalis repeated, lowering her head until she was on eye-level with Twilight.
"No."
Chrysalis ground her teeth together in fury. "WHY NOT?"
"I've never seen anything like you before, it's my duty as Princess Celestia's student to report any unusual phenomena." Twilight replied nonchalantly.
"WHAT!" Chrysalis roared as she transformed into an adult female wyvern, the bats scattering as green flames engulfed her form. Then she realized her mistake, she had forgotten to disguise her voice.
Twilight Sparkle looked up instantly, eyes wide open with terror. "C-Ch-Chrysalis?" She stuttered. Twilight might have stood up against her before, but this was the one pony she had ever seen defeat Princess Celestia, and her friends weren't there.
Chrysalis took her chance to escape while Twilight was paralyzed with fear, and quickly took to the skies, still in the shape of a wyvren.
~~~~~~~
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there's NO way i'm not reading this
Oh ho ho!! Now THIS is an interesting take on the origins of the Changelings! I remember Flutter Valley and the flutterponies from my childhood, back when I watched G1 My Little Pony. Nice little gen-crossing tie-in, there!
There are a few grammatical errors here and there, mostly just moments where your phrasing seems just a smidge awkward, but I enjoyed this first chapter enough that they didn't really matter to me. This story is going in my favorites, and YOU, missy, are getting a watch! 
Now, I'm not necessarily one way or the other on Chrysalis/Twilight, but your writing style is pretty fun, and your plot concept is interesting.
3533206 So you are reading it? Double negatives for the win!
3533215 Thanks! I'm glad you enjoyed it! I never actually watched 1st or 2nd gen, but I've picked up a few things from other authors. I've only watched the parts of gen 3 I can find on YouTube (if only there was more!) And gen 4. I actually wish I was a girl sometimes, but sadly I'm not. So yeah, I'm not exactly a missy... Lol... (I'm weird, I know).
3533286 I'm adopting you in my mind as Queen Chrysalis, hence the "missy."
That's really awesome, and even if you've not watched any of it, I give you kudos regardless! 
(My apologies, as I should have explained that. I'm in the habit of assigning people nicknames in my head, and your icon sealed that matter for me before I could think more on the matter.)And hey, for someone who's not watched any of the previous gens, that's not a bad thing!3533323 That makes much more sense now, I'm sure we've all done that before. I would watch more if I could find more, but alas I cannot, so I am forced to learn from other authors.
Ooo~ I like this. No... I love it!
3533363
Again, my apologies for the confusion.
That's how I've learned about the FIM comic series.
Well, if you get a chance to watch any of Gen 1, I WILL recommend the pilot "movie," which is called "Escape From Castle Midnight." It was probably the best thing from the original series, and worth a watch. Gen 2... I personally think that you're not missing a lot as far as that is concerned, but that's just my personal opinion. I personally feel like Gen 2 had terrible writing. But hey, nothing wrong learning from others, either!
And once again, I look forward to more of your story here!
3533404 I'ts alright, no harm done. I'll be sure to look it up in my spare time, thanks for telling me about it! My update schedule is sporadic at best, but I do have an idea of where I want this to go so you shouldn't have to wait more then a week for me to update, maybe more, maybe less.
3533400 I'm glad you enjoyed it!
A little fast for my taste but I will follow and see where this goes.
3533495 Yeah, I'm not good with writing slow paced fanfics, which is why I prefer to write oneshots. If you hate fast paced then you'll despise the next chapter, it's like two months after this one. Time skips for the win!
enjoying this so far, looks really promising, can't wait for more!
3533975 I'm glad you enjoyed it! I've begun writing the 2nd chapter, can't say for sure when I'll finish it however.
defiantly keeping an eye on this one nice work.
3534666 Thank you! I'll do my best to not disappoint you on the next chapter. :D
cdn2.dualshockers.com/wp-content/uploads/2013/08/Curiosity-attention-django-meme.jpg
Mh... while it could come from your own imagination, the origins of your changlings are almost a one to one copy of "Miorror's Image" (minus the Discord part). Which is probably fine if you told the author.
Bats nesting on Chyrsalis? Unless Chyrsalis transform into some kind of cave or at least a stone, that's just not possible, if you consider equestrian nature at least slightly similar to our own.
The Everfree Forest is in the middle of Equestria if we are to belive the official maps. One could have used it as a border in the beginnings of pony fanfiction, but today it just seems lazy or uninformed.
1000 words are thin. While a prologue could be just that thin, for a good story your chapters should at least be thrice as thick (and I don't mean thrice more scenes, but more descriptions).
grammar and spelling seems fine.
not a bad attempt.
but well, read some of the big and popular fics and take them as examples how your fic should look like.
3540151 YES! You're amazing!
3540657
Naaah, I'm nerd. My horse is amazing, not me
3540668make more please
Bookmarked. Can't wait for more, if it comes
3543089 I'm currently editing the second chapter, it should be up in a little while.
3543093
Can't wait
3543100 Be warned, there is a two month time skip for bizarre reasons I'm still not quite sure of...lol
3543104
Won't be a problem. I enjoy filling the gaps myself
3543104
Magic!
So Chrysalis went a little bit...
(Wait for it...)
BATTY!