Most ponies in Equestria held that there were two genders. Fillies and colts grew up to become mares and stallions. A tag in your chromosomes marked whether or not you'd be a colt, just like a tag determined whether or not you'd have horns or wings. But for perhaps one in seventy, that wasn't quite how it worked.
At birth, she had been taken away from her parents. Her mother and father had gone into a panic, imagining their child to be deformed - or worse, stillborn. The doctors spent the better part of an hour with her, instruments here, measurements there. They tested her reactions, her breathing, her cries and how quickly she squinted when they shone lights into her eyes. One by one, syndromes were crossed off the list as they investigated and documented, taking the derivative of an infant. Eventually as they came to realize the little snowball of a foal before them was perfectly healthy. Save, of course, for one striking peculiarity.
When they brought her back, she had already fallen asleep, shaking off the trauma of birth, wrapped warmly in a quilt. Of course, her parents had demanded answers.
Your foal is fine. Unique, but fine.
You tell us this - but we still don't know if we had a colt or filly!
Well, Mr. and Mrs. Bolt, that's where your foal is unique...
Her parents had been told the exact specifics, learning everything modern medical science knew about her condition. Her parents learned that she (no, Mrs. Bolt, ‘she’ will do for now, if we have it wrong she will tell us soon enough) was going to grow up as any other pony. She’d be awkward and silly. She’d get in trouble and have crushes and get sick and ask silly questions and be frustrating and occasionally infuriating and her parents were going to love her so much their heart would burst.
But Lightning Bolt was a very special pegasus. Lightning Bolt was one of the special one in seventy.
On the first day of kindergarten, Lightning Bolt was given a set of overalls. She didn’t like the itchy denim, and immediately tried to fly them out the window and drop them into the river below, where an earth pony who might enjoy a set of overalls would find them. But her mother, Ginger Bolt, wouldn’t have any of it.
It’s for your own good, Lightning dear. Little foals can be very cruel.
It’s because you’re different from them, dear. Most of them will be... typical. They don’t have the parts Mommy has and the parts Daddy has... they have only one or the other. And if they see, they'll know, and they'll be mean.
But as long as you have these on, dear, you’ll never be seen as different. You’ll just be normal, like any other pony there.
Thus, Lightning Bolt learned she was a different kind of pony. She learned fillies were mean towards each other, and mean towards colts. She learned colts were mean towards each other, and mean towards fillies. And she learned she didn’t like thinking of herself as one of either group a lot.
And so, Lightning Bolt went her own way, part of no tribe save her own. She studied hard; she got good grades; but mostly, she kept out of the way, and she kept quiet.
She followed in the wake of the moving van, gliding on the wake it left. She could have rode with the family's possessions, but after the events at P.S. 63, she felt like being in the air for a long, long time.
Puberty had taken its sweet time coming to Lightning Bolt, and it was indicisive. Her voice didn’t really drop, and her curves never really changed. But when it came, just like it had for all her classmates, it carried with it a dedicated interest in colts and in fillies.
The first filly she had set her eyes on, Sandstone, had been hewn out of much the same cloth as Lightning Bolt herself. They were both bookish and introspective, and looked forwards to adulthood as an escape from the stresses of childhood. Studying became friendship. Friendship turned into attraction. And, being young, attraction was acted on.
Sandstone never again talked to her after that day. But Sandstone had confided in someone, who hadn't kept Lightning Bolt's secret in confidence. Rumors spread after that, which reached other students - and their parents. Letters were addressed to the school board and to "the Bolt residence." Lightning Bolt's parents had a lot of talks behind closed doors; her father would grumble, her mother would shout, and both would sigh.
Eventually, they both came to the same conclusion - it would be easier if they just left Manehattan for somewhere quieter. Shetlandale would be a nice, small town to raise a filly in - small enough that her parents could keep a watchful eye over everypony Lightning Bolt interacted with.
Perhaps this time you'll keep your overalls on and your legs closed, young lady.
She listened halfheartedly to her parent's lectures. But Sandstone had already taught Lightning Bolt a much more important lesson - don't open your heart to anyone.
"Well, to be frank, this was all just a formality. Your grades and your trial run make you the most qualified. Want the job?"
Lightning Bolt grinned, and almost bounced on her hooves. "Are you serious?"
"We've lost so many ponies I can't afford to joke about this," Rainbow Dash said with only a hint of crossness to her voice. "It's not glamorous and you'll be sweating outside all day long, but the pay's good for a first job - and at the rate we churn through ponies, you can be guaranteed work. So long as you can keep up, that is," her new boss smirked.
"Then I'll take it," Lightning Bolt said, pouncing on the chance. "So. When do I start?"
"Way I see it, we hired you this morning. You busted those clouds harder than some of my regulars - call it four hours today and we get you on the schedule starting next week?"
"Awesome! Thank you so much - I won't let you down, Miss Dash."
"Pffft. You don't have to call me that. Rainbow Dash, Rainbow, Dash, Chief, Dashie, Boss, The Dash, RD, whatever's fine. I'm about the last pony in Ponyville you can call 'miss.'"
"Well then, I'll do my best to make The Dash proud," the white pegasus giggled, soon joined by her new boss's laughter.
"'The Dash' already likes your attitude - you're gonna do just fine. Just gotta fill out some paperwork for the paper-pounders in Canterlot." Rainbow Dash reached into her old 'desk' and slid a sheaf of paperwork over to her new hire. "Since this is your first job, most of this'll be empty - but hey, I already hired you, so don't worry none about selling yourself. Just fill in whatever you've got."
"Good. I didn't think you'd throw me out for having a terrible application," Lightning Bolt smirked. She filled in her contact details, the address of her tiny cottage on the outside of town and the distant contacts that formed her meager references, then handed it back to Rainbow Dash.
Her new boss took one look at the application, and smirked. "Huh. Just one little oversight here..."
Lightning Bolt tilted her head. "What do you mean...?"
Rainbow Dash pulled out one sheet, and passed it back. "Gotta check a box there."
Lightning Bolt looked down at the paperwork and grimaced. "Ah. Well..."
"It's easy. M or S, Mare or Stallion," Rainbow Dash shrugged.
She cringed, looking back to the form then to Rainbow Dash. "I... I can't do that, boss," Lightning Bolt said, pushing the paper back. "Sorry..."
"Huh. Easy enough for me to do," Rainbow Dash said. "Just need a check in the box here and-"
"Wait!"
Rainbow Dash quirked an eyebrow. "Wait what?"
"Don't - just don't. Leave them blank."
"Why? It's just for statistics, you know, it's not like they'll send a doctor out to check..."
Lightning Bolt grimaced at that turn of phrase. "Can't you just... leave it blank?"
"I... guess I could," Rainbow Dash agreed, frowning. "But I gotta ask... why?"
Lightning Bolt gave an awkward grin. "It's because I'm... different."
"Oh. Huh." Rainbow Dash's face betrayed mild surprise, but only for a moment, and she shrugged. "Okay."
"Okay?" Lightning Bolt sputtered. "Okay? Aren't you going to start with the twenty questions...?"
"Huh? Oh, no not really." Rainbow Dash shook her head. "Wait. One, I guess. Uhm- is it the condition that affects your heart?"
"Uhm... no. I don't have any issues with that."
"Didn't think so, seeing you buck those clouds. But I hadda ask," Rainbow Dash said. Then, she smirked. "Don't worry about the form. I'll send it blank, and if they throw a hissy fit, I'll tell them to take their statistics and stuff 'em in their chairs."
"Heh. Thanks, boss," Lightning Bolt smiled. "Well, there goes my biggest worry."
Rainbow Dash laughed. "Far from support from Canterlot, right off the wild weather of the Everfree, both rural and urban weather patterns in close proximity, and you're worried about how to check a box? We gotta loosen you up or you'll break down by your third day."
Lightning Bolt smirked. "I think I'm built a bit stronger than that, boss."
"Well, you're not alone, you know."
Lightning Bolt tilted her head. "Huh?"
"Well... there's a few others like you out here in Ponyville. Fluttershy's been my friend since flight camp. Caramel looks and sounds like your standard colt, but he talks with Fluttershy sometimes. Bon Bon runs the candy shop, and she's pretty open about it, but lemme warn you, if you let her know she'll probably talk your ear off."
"Huh... really, she just... and everyone knows?"
"Sure she does, and sure they do. What's wrong with that?"
"Well..." Lightning Bolt's wings shuffled uncomfortably. "I've... never actually talked to anypony else like me."
"Heh. Well, that's the nice thing about Ponyville, there's weirdness of all sorts busting out at the seams and we still all basically get along." Rainbow Dash wrapped a hoof around Lightning Bolt and gave her a little squeeze. "Now hey, trainee, come on; if you're going to worry so much about meeting ponies around town, I got someone you gotta meet."
"What?" Lightning Bolt squinted skeptically. "Is it some sort of shrink...?"
"Huh? Nah, nothing like that. Just my PFF Pinkie Pie. Trust me, the sooner she meets you and you get her welcome out of the way, the better it is for everypony..."
Lightning Bolt had finished outfitting her tiny house. Setting up a kitchen, a bed, and moving two crates of books wasn't that hard, after all. The pegasus flopped back on the bed and stared up, looking at the ceiling - the ceiling she had paid for with the rent she had earned with her own hooves.
"Heh. Guess this is what being grown-up feels like..."
She pondered taking a bit of a nap, just laying in the sun - but there soon came a knocking at the door. Lightning Bolt squeaked as one flap of her wings knocked her airborne.
"What was that...?"
Flittering out of her room, Lightning Bolt was only slighty squeaky when the door knocked again, three quick raps.
"I didn't ask for anyone..."
When she opened the door, she tilted her head at the gray pegasus. "Oh... mail, right!"
"Ayep! Derpy Hooves, mailmare third class, at your service," the laden pegasus said, dropping off a package. "Miss Lightning Bolt?"
"That's me."
"Well, you've got the big box today." The mailmare produced the package from the most overloaded pocket in her uniform, and provided a delivery receipt to sign. "Looks like a care package from home, if I'm not mistaken."
Lightning Bolt took the pen in her lips, and quickly scribbled out a reasonable facsimile of a signature. "Really? How can you tell?"
Derpy giggled. "Because A, the senders are Ginger and Running Bolt, and B, it smells like chocolate."
"Ah. Well, guess you can't argue with chocolate. Well, thank you, Miss Hooves-"
"Hey, before I go - can I ask you something?"
"Huh? Oh, sure..."
"It's just that..." Derpy cringed, doing her best to cover it with a smile. "Overalls are not a good look on you. And... really, doesn't it hurt when you fly?"
Lightning Bolt grinned wide, which looked more like a grimace. "Not... really. Besides, I'm used to it."
"You're used to it?" Derpy drew her breath in sharply. "Ow. I can't even imagine!"
Lightning Bolt shook her head. "It... stops ponies from asking too many questions."
Derpy took one look back towards Lighting Bolt's hindquarters, then back to Lightning Bolt, and nodded. "Ohhhh! I see. I understand completely."
"You... do?"
"I know how it feels," Derpy said, giving her bravest smile. "And... Ponyville's a good town. Mares like you and I don't have to worry about that too much."
Lightning Bolt's jaw dropped. "Like you and I?"
"Sure! I mean, here, look at my cutie mark," Derpy said, as she presented her flank. Lightning Bolt managed to pick her jaw back up as she realized that Derpy hadn't quite caught her meaning, but said nothing. "My special talent's making sandcastles at the beach! Just about as useless a talent as you can get, and ponies here treat me just fine."
"Ah. My talent is... well... knocking lightning bolts out of clouds. Not useful at all," Lightning Bolt said. "I guess you could guess that from the name. But... some ponies make mean spirited comments, so I keep covered up."
"Some ponies make mean comments? Really?" Derpy rolled her eyes, each rotating in different directions. "You don't say."
Lightning Bolt cringed gently.
Derpy smirked. "But you can't let them get to you, hon. That's the price of being happy. They can't get you down if you don't care."
"I don't know," Lightning Bolt sighed. "My thing is kinda big..."
"Seriously, you want proof?" Derpy grinned slyly. "It's market day in town. See for yourself - just mingle, do some shopping. Just do your thing, and I'm ninety percent positive nobody will bother you, even without those overalls."
"Ninety percent positive?"
"Well... okay. Less than ninety percent, depending. Have you met Pinkie Pie yet?"
She didn't take Derpy's challenge immediately, or the day after. In fact, an entire week had gone by, until the next market day. But a week had gone by, and nothing untowards had happened.
Well, she had learned a few things. Cloud Kicker was a good drinking buddy. Rainbow Dash was a sleepy drinking buddy. Fluttershy vouched for the kindness of the town, even if she seemed to be even more reserved than Lightning Bolt. Raindrops had pulled her aside and cautiously asked about pronouns during a break, but that was the beginning and the end of discussion on the topic.
So, Lightning Bolt decided to risk it.
After a quick bath, she brushed her fur out and preened herself clean. For years, she had gone straight from toweling off to slipping into her concealing overalls, so the brush found lots of tangles and snarls. Her hair was a permanently snarled mess, and convincing it to curl off to one side or another was about the best she could manage on short order. But when she reared up and looked into the mirror, a fairly normal pegasus looked back at her.
She couldn't help but grin.
Flight came much easier - without having to deal with the strap of denim between her wings, she was able to flap her wings at full extension. Instead of her usual quick wingbeats, she beat her wings in slow, powerful motions, making the climb far easier.
At first, she circled Ponyville from the air, staying at about cloud height. But then, a rush of pink and green flew past her, and Lightning Bolt spun around in place.
"Hey!" the pink-and-green blur said, as it slowed down and became Blossomforth. "Got the day off?"
"Yeah," Lightning Bolt said, as she slowly came to flying upright again. Well, if anypony's going to say something, it'll probably be her... She gulped, realizing that there really was nothing hiding her secret. And it'll probably be now. "Just... going into market, you know."
"Market day as your day off? Your first week? The boss must like you," Blossomforth said, shrugging. "Eh, have fun for me then, 'kay?"
Lightning Bolt smiled weakly. "Can do." She waited as Blossomforth flew off to return to her shift, and blinked.
"That went..." She grinned softly. "Pretty well."
Lightning Bolt went back over town. Looking around, the atmosphere wasn't quite festive, but ponies definitely came out to see and be seen. Stalls carried everything from basic staples to quick snacks to needless luxuries, and laughter and shouts ran out over the crowd. Traffic picked up in the Ponyville airspace, as a pegasi would occasionally launch up or come at her from behind and pass her - but not so much as an appraising glance came from any of them.
She hadn't been in a crowd this large since high school.
As she came in low over Main Street, she folded her wings back into a tight V formation, slowing her forward flight in a completely unnecessary, yet completely fulfilling barrel roll. Unlike how she had been raised, she wasn't the outcast; she wasn't the talk of the town, she wasn't using her parents or her grades as a shield from the world. Nobody looked at her and cast their glance just below her cutie mark, whispering to each other - although more than a few gave her a friendly wave as she flew on by.
For the first time in her life, Lightning Bolt was just another pony in the crowd. And she was free to do what she always wanted.
So she laughed.
Author's Note
This story is my entry for the 2013 Futaquestria Writing Contest, which has the following two requirements: (1) 'Acceptance' as a central theme; and (2) a background pony as the main character. Tying the ending in to the opening of Friendship Is Magic was just indulgence on my part. Marked as mature out of an abundance of caution due to subject matter and the group in question.
P.S. Lightning Bolt is best pony.