Her Rainbow Mane

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Applejack sat alone in the field, nervously tapping her hooves together. Many clouds in the sky hovered past, but only one stood stationary; the home of one of her best friends. A friend whom she feared that what she was about to do would change everything about them for the worst.
Almost everyone in Ponyville knew of Applejack, most of whom had strong opinions for the hardworking farmpony. Whether it be supplying the town with its food supply, lending a helping hoof to anypony in need, or for all the adventures and sacrifices she’s endured for so many others, many respected Applejack as a strong, iron-willed pony always blazing through life and putting others before herself.
She took all the praise with modesty; although she was flattered by the attention, Applejack refused to try and build herself up as something more than any other pony.
A gulp traveled down her throat. For the first time in a long while, Applejack wished that everything they said about her was true.
“You mean, you’re…but we’ve…” Rainbow Dash’s voice echoed in her head, tinged with shock. “I…I gotta go!”
Applejack cringed again at the image of Rainbow flying away. For a moment, she wished Rainbow wasn’t a Pegasus.
Her friends almost knew everything about her. She wasn’t one to keep secrets, and would often confide anything that was troubling or eating away at her. She always feared living some sort of double life, one she wore in public and one she’d lock away in her closet.
…that’d probably done the exact opposite for her.
Of all the things she’d told them, probably the one she’d tried so desperately to keep to herself was the biggest of all. One that always tugged at her heart as she talked with her friends. One that she’d feared could shake the foundations of what the six of them shared, especially her friendly rival Rainbow Dash.
The only pony that she could confide her secret to was Twilight Sparkle, her bookish companion.
“Why are you scared to tell her?” She inquired as she got over the surprise.
“I’m scared, ‘cause…what if she doesn’t love mares like I do and think’s I’m some kind’a weirdo? What’f she doesn’t even wanna be friends with me anymore ‘cause I’m a fillyfooler?”
“Well, Applejack, I’m not sure if Rainbow’s a ‘fillyfooler’ or not, or even if she would want to tie the knot if she found out you were one.” Applejack scratched the back of her neck at the memory.
“But remember one thing!” Twilight continued. “Even if she doesn’t feel the same way, I can assure you that Rainbow Dash is a lot kinder than many ponies think of her. She might be rough here and there, but she also cares deeply about lots of ponies, especially us!”
“Doesn’t mean it wouldn’t come as a big shock ta her…”
“Well…I’m certain that as surprised as she’d be at whatever you’d say, Rainbow Dash truly cares for you, whether it be as friends or…maybe lovers.” Twilight trotted to Applejack’s side, gently reaching around her shoulder. “I know that you’re scared, Applejack, and I can understand why. But I think you should at least tell Rainbow Dash how you feel.”
“Y…Ya sure, Twi?”
“Not just to see how Rainbow Dash would feel, but for yourself. I can tell that whatever fear you’re feeling is eating away at you, and telling Rainbow would solve things between the two of you.”
“I…I guess you’re right. I’ll tell ‘er.”
Twilight gave a smile and pulled her into a gentle hug.
“Don’t worry, Applejack. I promise that through even the worst, Rainbow Dash will still be your friend. I promise.”
A day later, Applejack sat looking at the clouds in fear.
“Maybe we won’t git together…” She sighed to herself. “…but please still be my friend.”
She sat there in silence for several minutes , the area silent aside from the wind sweeping through the field around her. However, her eyes widened as a blue, somewhat colorful blob shot out of the cloud home and began to descend towards her.
With somewhat a flourish, Rainbow landed with a gentle swoop, folding her wings in midair before expertly landing on four hooves. She had somewhat a proud look that Applejack couldn’t help but smile at.
“Hey, AJ! ‘sup?”
“Not much, Rainbow. You?”
“Eh, same old, same old.” She shrugged as she seated herself on the log next to applejack, just as peppy and friendly as always. Applejack loved that about her; she silently prayed this wouldn’t be the last time Rainbow acted like that around her.
“So, you wanted to talk about something?”
“Uh…yeah, Rainbow. I do.”
“You okay? You look kinda nervous.”
“Uh…well, Rainbow…” Applejack stammered, having no idea where to begin.
“Well, Rainbow…I know this might come as strange ta ya, but…whaddya think of me?”
“…What do I think of you?” Rainbow parroted, not expecting Applejack to be this upfront.
“Like…how good’a friends are we?”
“Well, uh…” She scratched at the back of her neck, not one for heartfelt discussion. “Well, I think that even though we don’t get along all the time, you’re a really nice pony, and all.”
“…anythin’ else?”
“Well, you’re as much my friend as the others are, and you’re my best friends. Why?”
“Uh…well, Rainbow, the truth is…I’ve kept a secret from lots o’ ponies.”
“What kind of secret?”
“Before I can tell ya, I just wanna know…” The conversation felt like a spinning top for Applejack, which any wrong word could topple over. “…would we still have a chance o’ bein’ friends?”
“Uh…” Rainbow Dash looked completely taken off guard. “What is it? Did you kill somepony, or something?” She let out a small chuckle, trying to diffuse the situation.
“…Rainbow…” It could’ve been seconds, even minutes that had passed before Applejack spoke again. She couldn’t tell. “Rainbow…I’m a fillyfooler.”
“…A Fillyfooler?” Rainbow Dash seemed surprised, but didn’t express any visible disgust or hatred. “…Really?”
“Yeah. I’m gay.”
“Woah…” Rainbow awkwardly scratched at her mane. “Is…Did you just find out, or something?”
“Nah, I’d…I’d know since I was a lil’ filly. Just never really got with stallions, s’all.”
“Huh…” Rainbow looked down at her hooves over the log, gently tapping them together. “…I’d never guessed.”
Applejack couldn’t read Rainbow’s face as another silence passed between them.
“So what?”
“Whaddya think?”
“I’m surprised, I guess…”
“You don’t hate me, or anythin’?”
“…Is that what you’re worried about?” Rainbow replied with a somber expression. “Of course not!”
“So we’re still friends?”
Rainbow rolled her eyes and smiled, letting out a cackle.
Duh, we’re still friends!”
Despite Rainbow’s lighthearted reaction, Applejack surprised her and pulled her in for a hug, a wide smile on her face as slivers of tears began to appear on her lashes.
“Thank ya, Rainbow…” She insisted as Rainbow softly returned the hug. “Thank ya’ll so much…”
“Hey, no prob. It can take a lot of guts to come out with stuff like that.” As they slowly broke the hug, Rainbow giggled at the tears streaming from Applejack’s eyes, who chuckled too as she wiped at her damp cheeks.
“So, anypony else know?”
“Only Twi…but there’s more.” Applejack knew she was only halfway out of the woods. “I…think there’s somethin’ else y’all should know, Rainbow.”
“What else?” Rainbow didn’t seem to understand what could top that. She’d realize how wrong she was.
“Rainbow…before I say anythin’ else, I just want y’all to know that I truly love what we have as friends, and…I hope what I say won’t make things hard b’tween us…”
“Applejack, I just said things are cool between us!”
“Ah know, but… fer everythin’ we’ve gone through, all the good times we’ve shared, all the time where we talked, an’ all…” She paused, wishing she were a more eloquent speaker. “I just…fer all the time’s we’ve been together few a while…there was somethin’ more. Somethin’ I always thought would be real only in my dreams, but…but hope ta make real.”
…and there it was.
Something flared within Rainbow’s eyes. Something that seemed to cease any imperfection in the world, and brought an image she’d long though a dream into solid, emotional reality.
“A…Applejack…Are you saying?” Rainbow stammered with a look of astonishment. With as much confidence as she could muster, Applejack smiled and slowly nodded, more tears streaming from her eyes.  
Rainbow smiled.
“Can…” She began with anticipation, reaching for Applejack’s hooves, one in each as she looked into her eyes. “…can you say it?”
This was it. Every bit of joy in the world belonged to her as everything Applejack feared died on sight. She paused, cherishing the moment as she looked straight into Rainbow’s beautiful, warm, hopeful eyes. Her lips tensed, filled with anticipation at the words to come out.
“…I love ya, Rainbow.”
But Applejack’s smile slowly melted as Rainbow Dash’s eyes began to glow a bright white, prompting her to gasp as the two of them slowly began to float a few feet off the ground. A faint whining sound around them became louder and louder as Applejack tried to wrench herself out of Rainbow’s grasp, but found herself trapped in her vise-like grip as a beam of blinding white light shot from Rainbow’s eyes and into hers. She tried to let out a scream that instantly faded as her face completely relaxed, transfixed within Rainbow’s gaze.
The colors of Rainbow’s mane seemed to begin to shift, but still maintained their separate contrasts as they began to seep off her scalp, traveling down her neck and past her shoulders whilst the two ponies remained frozen in midair with a blinding white aura around them. The colors trickled across rainbow’s legs, traveling across her hooves and not stopping as they transcended upon Applejack’s. The instant they managed to flee Rainbow’s body completely, the two ponies were flown back as a massive explosion of energy thundered between them, sending the two back several feet and knocking them out cold.

A cyan pony whom nopony in Ponyville had ever met before lay unconscious in a field. She slowly stirred awake, with only fragments of what’d just transpired floating in her mind.
“What just…” She groaned as she weakly got onto her hooves, slowly adapting to where she was. An orange blob laid some distance away. As she approached to see what it was, she let out a gasp as found it to be an orange earth pony with a familiar spectral mane.
She flew over to a nearby pond, tears forming in her eyes as she saw her jet-black mane in the reflection.
“I…I’m free!” She joyfully exclaimed. “I’m free! I’M FINALLY FREE!
With an elated smile, the Pegasus took off for the sky, her howls of sheer  
joy fading in the distance.
The orange pony groaned as she awoke minutes later, thoughts of the Wonderbolts and Daring Do bouncing in her head. With a somewhat lazy look, she groggily stood up and headed back towards ponyville.
Twilight looked up from her book as the door to the library chimed open.
“Hello, Applejack! How’d things go…with…” Her smile faded as she noticed Applejack’s rainbow-colored mane.
“Eh.” She stated simply. “She’s act’ally kinda lame.”
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Burger Rebellion
Nice so far…I’m no critic but you should work on bringing in different characters and transitions but other than that it’s cool, please continue the story

You have a good style, the story is quite interesting. It’s a pity that you didn’t want to make something more out of this story.
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