Part 2: Flying is Impossible!
It was a fine evening in Ponyville. As the sun began to sink gently towards the western horizon, Rainbow Dash broke up all the afternoon clouds to give all the ponies a lovely view. When she flew over the library, however, something strange happened. She began to fall into a tailspin. Frantically, Rainbow tried to flap her wings to gain some altitude, but there was no response. She tumbled through a window and bounced across the floor of the library. Twilight saw her land and asked, “Are you all right, Rainbow? That looked like a nasty fall.”
“Yeah, I'm all right,” she replied. She brushed herself off, commenting, “I've never had that happen before! It was the weirdest thing. My wings just suddenly gave out on me. I must be tired.”
“No, it's probably more because of this.” Twilight lifted up her paper with a hoof. Rainbow walked over to look at it.
“What am I looking at?” she asked. “All I see are a bunch of squiggles and a picture of a pegasus.”
“They're my calculations about pony flight. Taking into account the length and breadth of pegasus wings, the mass of an average pegasus, and the necessary amount of lift that would be required to propel a pegasus anywhere in the sky, I've firmly concluded that flight by pegasi is impossible. There's simply no way that a non-aerodynamic equine could fly.”
“But... we do.” Rainbow scratched her head as she searched for an answer. “I think it has to do with magic or something?”
“Ah, but I disproved magic this morning, too,” Twilight said. “You'll need better proof than that to convince me.”
“You... disproved magic?” Rainbow Dash fell to the ground and guffawed. “You've got to be kidding me! Miss Magic disproved her own talent? That's hilarious!”
“Oh, believe me, I'm just getting started,” she said in return. “This whole thing has really fascinated me! The basic qualities of our universe are completely implausible. After I get this flight stuff done, I'm moving on to melanin and keratin production.”
“Melons and carrots? What do those have to do with anything?”
“Not melons and carrots. Melanin and keratin. Melanin is the protein that creates the pigment in our skin, while keratin is the primary component of our hair, hooves, and horns.”
“I still don't understand.”
Twilight sighed. It was hard being a genius. “Purple! Green! Blue! Those are not natural colors that keratin can produce! How can our tails, coats, and manes be such strange colors? It doesn't seem to make sense!”
“It just does! It's probably because of... magic...” Rainbow suddenly realized just how deep this rabbit hole might be going.
“Wrong! Magic is impossible! And if magic is impossible, what else is too?” Twilight asked. “Now, if you don't have anything else to tell me, please excuse me. I have a lot of work to do.”
“All right. See ya, Twi,” Rainbow Dash replied. She flapped her wings, but she couldn't get up into the air. Something wasn't right. She had taken off hundreds of times before, and she'd never had trouble like this. Even when she'd had her wings flipped by Poison Joke, she could still take off and fly, albeit like a drunken seagull. But this? What the hay was going on? Could Twilight be... right?
Was flying really impossible?
Her eyes started to well up with tears. Flying was her life, her dream. What was she going to do if she could never fly again? She ran out from the library, trying to keep Twilight from hearing her sob. Eventually, she ran into Applejack, who was out in the market. “Applejack! I can't fly anymore!” she told her.
“What? Why not?” Applejack asked.
“Twilight told me so!”
“Hoo boy,” Applejack said. She stretched out her limbs, then put a “closed” sign on her stand. “So she got to you too, huh? I heard 'bout Rarity and her magic.”
“Twilight was telling me about that! She disproved magic? What does that even mean?”
“I don't know, but whatever she's doing, she's gotten real convincing. We've got to get Twilight to stop telling ponies those lies.”
“That's the thing!” Rainbow said, her eyes wide. “I lost my flight before she told me it was impossible! Somehow it's spreading!”
“You've got to be kidding,” AJ replied. “That ain't good at all. Then we may have bigger fish t'fry. Ah think we've got to get to Cloudsdale before her 'Logic' does. You go do that, and Ah'll talk to Twilight.”
“You got it!” Rainbow threw her a salute, then raced off to find a hot air balloon.
Applejack made her way to the library. As soon as she touched the door, the hairs on the back of her neck began to prickle. There was something very unright about this whole situation. The first thing she saw was Twilight, who was working feverishly at her desk. She had expanded it to include about three tables, and everything was coated with an even layer of paper and writing implements. She walked straight up to Twilight and asked her, “What the hay are you doing, Twi? You've really gone off the deep end.”
“Hello, AJ,” Twilight replied, her tone cheerier than Applejack's mood warranted. “Right now, I'm studying earth pony mass. I was doing a proof about pegasus cloudwalking abilities, but I got sidetracked. Did you know there's no way you could have propelled Rainbow Dash that far, back during Applebuck Season? Earth pony mass is completely impossible.”
“Oh, really? And just what does that mean, then?”
“Well, I haven't fully decided, but I think it means you and all earth ponies weigh the same as other ponies; any evidence to the contrary is ridiculous fantasy.”
“Twilight, you can't just go around saying what must be and assumin' the world will match your way of thinkin'.” Applejack tried to ignore the feeling of lightness that was overcoming her. “This whole anti-magic thing you've got going is just not healthy.”
“What? Searching for the truth?!” Twilight raised her voice. “I'll keep on searching until I understand the world perfectly! I must know how and why everything works the way it does! To do any less would be to shame the legacy of science itself!”
“Okay, I think you need to go to bed.” Applejack held her close and helped her out of her seat.
“Wait, just one last thing.” She grabbed the pen with her mouth and wrote, “It's apparent that clouds, being clusters of water vapor and not solid products, cannot be stood upon like ground. It's impossible, therefore, for pegasi, or other ponies using a cloudwalking spell, to stand upon it.” With that done, she set the quill back down and consented to let Applejack drive her up to her soft bed.
***
Later, Applejack called together a meeting of the other five Bearers to discuss the problem. “What do you suggest we do, y'all?” she asked them. “She's ain't listenin' to anything approximatin' reason. She's obsessed about this darn idea that magic is impossible, and I don't know if there's any way to stop her.”
“She... may be right,” said Rarity. The other four looked at her, astonished. “What?” she asked. “Ever since she told me that magic is impossible, I haven't been able to use it. I've taken the liberty of looking through her notes, and, well, she's quite convincing. There really isn't anything in the unicorn physiology to suggest the abilities we assume.”
“Then how were we able to do it before?” Rainbow Dash asked. “How could we do something impossible?”
“I don't know. Ignorance is bliss, perhaps?” Rarity answered. “Or perhaps Twilight has finally made the universe notice its error.”
“But how will the pegasi control the weather if they can't fly or stand on the clouds?” Pinkie asked.
“That's the strangest thing.” Rarity pulled out a paper from Twilight's desk. “She has these things here she calls 'warm fronts' and 'cold fronts.' Apparently, differences in temperature create them, and when they move, they create weather.”
“So you're saying...”
“Yes. Controlling the weather is impossible. It's far too complex and microscopic to be changed by pony hooves.”
“Oh no...” Fluttershy murmured.
“What, dear?” Rarity asked her.
“Oh, it's just... what if Princess Celestia finds out about this?” she asked them.
“Or worse... what if Twilight disproves that Celestia and Luna move the sun and moon?” Rainbow added.
“Uhh... gals?” Applejack said. “I think she may be working on it.” She pulled out another piece of paper. “She's got somethin' written here 'bout elliptical orbits 'n heliocentrism. It ain't done yet, but if she finishes it...”
“She may just prove it.” Rarity shivered. “The very cornerstone of our way of life. The authority by which Celestia and Luna rule. Gone. We can't let her keep working on this.”
“But... what do we do, then?” Fluttershy asked.
“Ooh! I know!” Pinkie answered. She pulled out a box of matches and a tank of kerosene. “Fire!” she said, with a wild grin across her face.
“I agree!” Rainbow said. “It's the only way!”
“As much as Ah hate to say it... Ah think they're right. Let's take 'em outside and git it done with.”
The flames drew up to the sky, reaching for the stars as they took Twilight's heresy far away.
***
Pinkie Pie whistled a happy tune as she went to Twilight's house the next morning. She didn't do it often, but when she did, it was a pleasure to burn. And it had helped Twilight so much, too! Now they wouldn't have to worry about any more crazy things happening or disappearing. She knocked twice on the door. “Hey, Twilight! It's me!” She pulled out a box of muffins. “Thought I'd bring some muffins to have breakfast with you!”
Pinkie heard the sound of the door unlatching, followed by it swinging open. But the pony who opened it looked nothing like Twilight. For one thing, she wasn't purple; she was brown. And not a nice even brown like some of the other ponies around town, but a spotted, dusty, uneven brown, marked with white and black spots. For another, she didn't have a horn or wings. When she saw Pinkie, she smiled. “Good morning! Come in, come in!”
“...Who are you?” Pinkie asked. “Do I know you?”
“Oh, silly, it's me, Twilight!” She laughed. “We've been friends for how long?”
“You don't look like Twilight. Twilight is purple,” Pinkie replied.
“No, I'm not. That's utterly impossible. Keratin can't possibly come out in purple! No, it makes much more sense for it to be like this.” She gestured to her coat proudly.
Pinkie stood stock still, her mouth agape. “But I... but we... your notes...”
“Oh, yes, I saw that.” She chuckled to herself. “Don't worry; I'm not mad anymore. You see, I had the most wonderful dream last night. As it turns out, I got most of the work I wanted to do done in there. And since I remember it all,” she said, tapping her head for emphasis, “lucid dreaming, eidetic memory, and all, I don't even need those notes any more. I just need to copy it down from what I remember! Ooh, those muffins smell delicious! Didn't I say you could come in?”
“Uhh...” The box of muffins fell from her nerveless hooves.
“That's another thing I'll have to tell you about. Did you know grabbing things with your hooves is impossible? I don't know how we never noticed it before.” She grabbed the box with her teeth and waved Pinkie in.
“I think I need to go send a letter,” Pinkie said nervously.
“Just ask Spike to do it,” Twilight said. Suddenly, she tipped her head to the side. “Wait a minute. How does his dragon fire even work? How could you breathe fire on something and make it--”
“Shut up!” Pinkie threw a hoof over Twilight's mouth. “Let's just eat our breakfast in peace without any world-ending science talk!”
Twilight nodded her head. They sat around the table, and for a moment, Pinkie could relax. She grabbed a cinnamon streusel muffin (her favorite) and set to devouring it. However, Twilight asked her, “Pinkie, do you dye your coat?”
She spit out the muffin in shock. “What? No! I'm a natural pink!” she replied. “Why do you think my parents would name me that if I wasn't?”
“Well, it's just that you're coming in brown,” Twilight replied. Pinkie looked at her coat in horror.
There, at the very base of the hair, was the color brown.
End of Part 2
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Uhoh
in BROWN??? 
Well, this can only get better.
TWILIGHT IS NOW THE WORD OF GOD
RUN BEFORE HER TRICKERY SPREADS
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Twilight knows she has wings, she just doesn't believe she can fly.
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What's PFA, and does she even still have her horn and wings? Also, I think the title of chapter 2 doesn't match the chapter. Great story, though!
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Pony Fiction Archive.
And... I don't have any other good name for the chapter, so... nyeh.
EDIT: Also, Twilight hadn't disproven flight yet at that point.
Well, this is an interesting twist :)
I like it
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Final chapter's coming up this evening. Hope you're super-excited!
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I am!
I was yelling at my laptop how things fly the entire chapter.
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Would it help if we know that pegasi don't taxi, and that they don't buzz their wings like bees? 
All right, I'll admit I'm not an aeronautics expert.
Well I theorized it last chapter, but I'm almost certain now. They have to kill Twilight.
Welp, this almost deserves a dark tag, since there seems to be no existential horror tag.
Ruh roh.
They just need to convince Twilight to prove that eidetic memory is impossible.
I'm loving this. Twilight has gone off the deep end, and the rest resorting to fire made me laugh.
And I had to rattle my head to imagine Twilight as a brown earth pony. That looked... weird.
I hope RD got to Cloudsdale in time.
God dammit Twilight! You're invoking as an Absolute Mundane. Stop it! Stop it right now!
Twilight's heresy... Lulz
You do realize color proteins other than melanin exist, right?
There are things in real life that are made out of keratin and purple.
Discord made magic happen. He’s the God of Chaos, he makes the impossible possible. But how is he possible, you ask? He made himself possible retroactively.
Wait until she gets to pony sentience...