Some things are best left unknown

by Xavier271

Rating: everyone
Tags: Twilight Sparkle, Sad, Drama, My Little Pony: Friendship is Magic, Rainbow Dash, Rarity, Romance, Fluttershy, Pinkie Pie
Length: 3305

Rainbow has been keeping a secret from her friends for years on end now, what would happen if they were to find out.

For years Rainbow has kept a secret from all of her friends, she has feared them finding out for as long as she can remember. What would happen if they were to find out. Rainbow's biggest fears are about to become true.

Published 2018-06-02 02:10:11 UTC
Last updated 2018-06-02 02:10:11 UTC

Chapter 1

Some things are best left unknown.

It was an exciting day for Rainbow Dash, possibly the best day ever as she had just been given an invitation to the wonderbolts and she just needed her passport and identification as a legal requirement to join the wonderbolts.

As soon as Rainbow had her letter delivered she instantly flew over to all her friends houses and informed them, Pinkie almost exploded when she found out. Rainbow invited all her friends over to her cloud house, which she was very proud of, Twilight simply cast a spell on herself, Pinkie, Applejack and Rarity to let them stand on the clouds just like when Rainbow was at the young flier's competition.

"They should be in this box somewhere" the young pegasus said, addressing Rarity.

"But these are all your confidential files Rainbow" replied Rarity.

"Rarity you're one of my best friends, I don't care if you see some of my files, just find my passport" the pegasus reassured.

"If you say so" said Rarity. When shuffling through all of the papers Rarity noticed that a large mass of these are medical papers about all the times Rainbow ended up in the hospital.

"Silly Rainbow" she thought to herself.

Suddenly Rarity noticed a different kind of medical paper, curiously, she looked closer at it. "CERTIFICATE OF TRANSGENDER OPERATION" this left Rarity extremely confused, why would Rainbow have another ponies transgender certificate, so she continued to read. "This is a valid document to certify Rainbow Blitz has undergone a transgender operation and has become a mare named Rainbow Dash" Rarity was in complete and utter shock.

"OH MY GOODNESS!" she screamed out loud gaining the attention of everypony in the room.

"What's wrong?" Rainbow enquired.

"Thi.t...t..wha..but...but..what?" She was at a loss of words.

"Are you feeling okay Rarity?"

"This is a certificate that states Rainbow Dash is transgender" Rarity's voice was stern and serious, when Dash heard this her eyes went wide and her heart began to beat really fast, everypony was staring at Rainbow, Fluttershy was fearing the worst, she knew one day they would find out.

"You're transgender?" Applejack demanded.

"How could you lie to us all for years?" Twilight was shocked.

"I've been speaking to a stallion all these years" at this thought Rarity almost gagged, Rainbow didn't know what to say, what to do, tears began forming in her eyes, her worst fear had become a reality.
Not knowing what to do she panicked and started breathing heavily, she had to get out of there, and in a flash she flew out of her door leaving a bright rainbow trail behind.

"How could she not tell us?" Applejack was furious.

"Because she didn't want to" Fluttershy's voice was much louder and much more serious than it usually is.

"You are okay with this?" Rarity was confused.

"Of course I am, and I have been for years!"

"You mean you knew about this?"

"I WAS THERE" Fluttershy was practically screaming.

"HOW COULD YOU KEEP THIS A SECRET FROM US"

"BECAUSE YOU WEREN'T SUPPOSED TO KNOW" she was now in tears and audibly crying.

"What's wrong with her being transgender?" Pinkie suddenly requested.

"The problem is that I have the right to know the gender of the pony I'm talking to" said Twilight.

"You made Rainbow cry, I hope you're happy, come on Pinkie let's go" and with this Fluttershy left through the door, and Pinkie quickly followed.

"Go to my cottage Pinkie, I'll meet you there later" Pinkie nodded, now all Fluttershy needed to do was find Rainbow Dash. Whenever Rainbow is sad she would always fly to her cloud house, however this time that's exactly where she was running from, so Fluttershy didn't know where to look, she had to be somewhere up in the sky she thought, and just as she was about to give up she noticed a rainbow tail sticking out of a lone cloud in the sky, immediately she flew over to it and there she saw Rainbow crying her eyes out.

In between her sobbing Fluttershy could hear Rainbow talking to herself.

"THEY ALL HATE ME!"

"WHY WAS I BORN LIKE THIS"

It tore Fluttershy's heart apart to watch and it caused tears to start dripping off her nose.

"Rainbow?" She said very gently, this instantly caught her attention and Rainbow immediately turned to look towards the source of the voice, she didn't know whether to run from Fluttershy or think of an excuse, accepting that there was no point in lying to her she broke down.

"Oh Fluttershy, they all hate me, I knew this would happen"

And Rainbow just started crying, seeing her best friend like this she leaned in to hug her, they were both crying and it was a heartfelt moment for both of them.

After a few minutes they broke the hug.

"Thanks Fluttershy, I needed that"

"It's fine, come down to my cottage, I think you will need somewhere to stay"

Rainbow nodded and both of the pegasi flew down towards Fluttershy's small cottage where Pinkie Pie had been waiting.

Upon arriving at her cottage, Fluttershy opened the door and walked inside, with Rainbow following behind, Fluttershy's cottage was rather small, but it was very cosy. Pinkie Pie was sitting on the sofa, she looked really worried and did not have her usual happy mood.

"Please don't freak out when you wal..."

"What's she doing here? Rainbow shouted getting ready to speed off.

" Rainbow please wait, let me explain"
With this Rainbow calmed down and reluctantly stepped inside.

"Pinkie here doesn't see anything wrong with you being transgender, she doesn't hate you." Fluttershy explained.

"I would never hate you Dashie, you are my friend and I would never judge you" Pinkie said putting her hoof around Rainbow's neck, the young pegasus breathed a breath of relief and embraced Pinkie into a hug.

"Thank you, thank you for accepting me for who I am" Rainbow cried tears of joy, she was terrified of losing her friends, and to know that one of them did not hate her was the best news she could hear.

"So it's true?" Pinkie asked nervously.

"Well I don't really want to talk about it, but yes, I was born a colt and I had a transgender operation when I was 12, but I just want to forget that it ever happened" Rainbow tried to be as vague as possible while talking about this topic, it was really painful for her to even think about it.

"Well that's okay Rainbow, it's not your fault" Pinkie responded.

"You can stay in my guest room for however long you want Dash" Fluttershy said.

"Thanks Fluttershy" Rainbow Dash trotted up the stairs of the cottage towards the guest room, it was a room Fluttershy very rarely used as she was usually too shy to have any guests stay at her cottage.

A few minutes later...

"I don't understand why the other girls are being such meanies" Pinkie said crossing her arms.

"I really don't kn...."

Fluttershy was cut short by loud knocking on the front door, she stood up and walked over to the door, even before she could open it there came more knocking, it was clear whoever was knocking was either angry or impatient. Fluttershy opened the door and was not happy with what she saw, Rarity, Applejack and Twilight were at her front step.

"We need to speak with Rainbow, right now, we know she's here" Twilight said angrily.

"You have no right to speak to her after how you treated her"
Fluttershy's voice was almost terrifying, it left a cold silence in the doorway.

"What?" All three ponies stated.

"You hurt her, you hurt her bad, now get out of my house"

"I'm not going anywhere until I have answers" Rarity demanded.

"LEAVE MY HOUSE!" Fluttershy slammed the door furiously and ran upstairs leaving Pinkie to sit there in shock.

Rainbow Dash heard what happened, she couldn't believe how Fluttershy stood up for her, seeing her run upstairs crying made her heart break, she was so courageous brave for her, but why? Fluttershy is always so incredibly shy and cute, she would never act li... Wait, did I just call Fluttershy cute? Why did I think that, i"m cool, I don't do cute, and why does she look so beautiful, why am I thinking these thoughts, she's my friend, I need some rest. And so Rainbow headed to bed.

After Fluttershy refused entry to three of her so called friends, they left, Rarity and Applejacked stormed off to their respective homes, and so did Twilight, but hearing what Fluttershy said actually dawned on her as she walked home.
"You hurt her" Those words made Twilight realise what she was doing was wrong, before this she was angry, she felt lied to by one of her best friends, she had intentions of going into Fluttershy's home and screaming at Rainbow, how could she even think of doing something like that, she was still her friend even if Rainbow was once a colt. She had just destroyed her friendship with both Rainbow and Fluttershy and she cried herself to sleep.

The next morning Rainbow awoke with a daze, during the night she couldn't stop thinking about Fluttershy, anything she thought about would link to her in any way "I need to talk to her about this" Rainbow got up from the guest bed and walked over to the door, she pulled it open, directly opposite the guest room is Fluttershy's room to which the door was open, she wasn't inside so she was already awake. Rainbow made her way downstairs, she could smell toasts cooking in the kitchen so she trotted over to the kitchen and swung the door open, there she was in all her beauty.

"Hey Fluttershy"

"Oh Rainbow, you're up, I'm cooking some toasts for us, how did you sleep?"

"I slept well, but I was thinking about yesterday"

"Oh..."

"You really stood up for me back there, thanks"

"You're welcome Rainbow, but I don't know what to do now, Pinkie must have left after I ran upstairs because she's not here and three of our friends are no longer our friends, I messed it all up" she said and started quietly sobbing.

"Hey you didn't mess anything up Fluttershy, that was very sweet of you, if they don't accept me for who I am, then they were never our true friends"

*sniff* "Really?" Rainbow hugged Fluttershy.

"Yes, don't worry about it"

"Okay" *sniff*

"There there" Rainbow stroked Fluttershy's mane.

"Okay it looks like the toasts are ready, so let's eat"

Rainbow and Fluttershy proceeded to eat their breakfast, when they were done Rainbow walked over to Fluttershy.
She came to a conclusion that she had fallen for Fluttershy, she could only think about wanting to be with her, and it was time to confess her love.

"Um, Fluttershy, I have something I need to tell you" Rainbow's sudden change of tone almost frightened the buttery pegasus.

"Oh, okay Rainbow, what do you want to tell me?"

"Well, you see, I was thinking lately, and basically, I sorta like you" Rainbow started blushing.

"Well I like you too, I thought you knew that"

"No Fluttershy, as in I like like you, as in I love you" Rainbow put her head in her hooves and feared the worst. She was expecting Fluttershy to either reject her or run away, but all she felt was a two hooves around her waist, Fluttershy was hugging Rainbow.

"You don't know how long I've been waiting to hear that Rainbow, I love you too and I always have, I was never brave enough to tell you" Fluttershy was crying tears of joy, for the past few months her crush on Rainbow had been tearing her apart, she was so glad to know she felt the same way.

"So are we a couple now?" Fluttershy asked.

"Looks that way" Rainbow responded.

"Well maybe we could go on a date" Rainbow continued.

"Okay, when?"

"Right now" Rainbow dashed forward and scooped up Fluttershy and flew towards the door.

"Rainbow!" Fluttershy screamed in shock.

"Don't worry Fluttershy I know a really good spot where we could hang out"

Rainbow carried Fluttershy in her arms all the way to a lakeside in a clearing, it was a beautiful place that very few ponies knew about, she safely placed Fluttershy down.

"Wow, this place is beautiful Rainbow"

"Not as beautiful as you" Fluttershy blushed.

"That's very cheesy rainbow"

"I know" Rainbow smiled.

The two lovers continued to talk for almost an hour before Rainbow got hungry and wanted to go to Fluttershy's home.

Rainbow and Fluttershy arrived at Fluttershy's cottage and went inside.

"So how was that Fluttershy?"

"Magical, I love spending time with you, because I love you"

"I love you too Flutters" Both of the pegasi looked into each others eyes as they slowly closed in, they both closed their eyes and their lips met, they held the passionate kiss for a few seconds. After they kissed they looked at each other, both of them had longed for this for so long, she would never admit it to herself by Rainbow had admired Fluttershy since flight school.

"That was"

"Amazing" Fluttershy finished Dash's sentence.

"How about we go snuggle in your bed"

"But it's just the afternoon!"

"Oh well we can take a nap"

"Okay!" Fluttershy ran upstairs ahead of Rainbow, which came as a shock to her.

"Hey! Wait for me!"

For the past few days, Twilight had not been coping very well, constant regret and guilt filled her thoughts at every point during the day, she had really messed up this time. "Some friend I am" she quietly said to herself.

"What's the matter Twilight, you seem down lately" Spike asked, Twilight had not mentioned anything that happened to Spike as she deemed him too young to understand such topics.

"I'm fine Spike" Twilight responded in a monotonous tone.

"No you aren't Twilight, I can see you are unhappy, you can tell me anything"

"No I can't spike, I can't tell you this, I just made a mistake, a big mistake, the biggest I've ever made and I need to fix it" Twilight quickly sped out of the room and made way for the door, leaving a very confused and worried dragon behind. Twilight knew what she needed to do, she had to find Rainbow so she spread her lavender wings and flew up into the sky.

Twilight had been searching for just short of two hours, she was exhausted, but she couldn't give up, she had been all over town six times, she had asked dozens if ponies if they had seen Rainbow, but she couldn't find her, nopony was even at Fluttershy's cottage or Rainbow's cloud house.

Suddenly, she saw her, just at the edge of the Everfree forest, she was walking on the ground, which was unusual for Rainbow, she always flies. Twilight descended slowly towards Rainbow ensuring she isn't spotted, she landed on the ground a few meters behind the pegasus.

"Rainbow?" Twilight said with uncertainty.
Rainbow turned to look behind her, when she spotted Twilight she panicked and spread her wings preparing to run away.

"Rainbow wait!" The pegasus ignored the command.

"Please" When hearing this Rainbow stopped in place and folded her wings, she could hear the desperation in Twilights voice.

"What do you want?" Rainbow responded angrily.

"Rainbow, I know you hate me, but please give me two minutes and I'll leave you alone permanently" Rainbow wanted to disagree and just fly off right then, but she decided to hear Twilight out.

"Ughh, fine"

"The way I acted was disgusting, I said things I shouldn't have said to you, I was angry and selfishly thinking about myself, without realising how much I was hurting you, as the princess of friendship my actions are shameful, I made the biggest mistake of my life that day, by overreacting over something as stupid as your gender, I don't deserve your forgiveness, but, I'm sorry"

Twilight began to tear up.

"I really am, goodbye rainbow Dash"

Twilight turned around and started walking away.

"Twilight"

Rainbow managed to catch Twilights attention.

"Do you really mean all that?" With tears streaming down her face Twilight said.

"Of course I do Rainbow, you were one of my best friends, and I really don't want to lose you, I will never judge you again, I'm so sorry"

"Okay, I forgive you Twilight"

"Really?" Twilight's eyes lit up. She was not expecting to hear that.

"Yeah, come here" Rainbow reassured and held her hooves out for a hug. Twilight threw herself into Rainbow's arms.

"I'm sorry Rainbow, I'm so sorry" Twilight sobbed into Rainbow's cyan fur.
"There there, it's okay, we all make mistakes, just don't get all sappy on me."

"Thank you"

"Let's go to Fluttershy's cottage" Rainbow opened her wings and lifted off the ground knocking Twilight to the ground."

"Come on Twilight, I taught you to fly" Rainbow chuckled and grinned.

"Hey I wasn't expecting that" Twilight rose from the ground.

"Follow me" Rainbow instructed.

The two ponies landed in front of the small cottage and Rainbow didn't hesitate to knock on the front door. Fluttershy walked over to the door and pulled it open.

"Hey Fluttershy"
"Hi Rainbo...." Fluttershy was shocked to see Twilight, and with Rainbow Dash?

"What's the matter Fluttershy, surprised?"

"Well...... Yes"

"Me and Twilight made up, she's apologized now and we are friends again"

"Oh that's wonderful Twilight, I'm glad you two are friends again"

"So am I, I couldn't cope with the guilt I felt, and I truly am sorry for the way I acted" The lavender mare responded.

"Well why don't we all go inside and have a sleepover to repair relations, I can invite Pinkie as well"

"That sounds like a great idea Fluttershy"

"Sure that's cool"

Later that evening Pinkie had arrived to join the sleepover at Fluttershy's house, the four ponies played several party games and talked with each other for several hours until at one point the conversation turned serious.

"So, um, what happened with Applejack and Rarity?" Fluttershy asked.

"I haven't seen or spoken to both much since the incident, it appears they have moved on" Twilight explained.

"Just like that? They just forgot about their friend? What kind of pony does that?" Rainbow vented her frustration.

"I haven't even seen both of them since" Pinkie added.

"Well it's late girls, and we best head to bed" Fluttershy stated.

"Alright I brought my sleeping bag" Pinkie pulled a sleeping bag from seemingly nowhere and rolled it out on the floor.

"Where will I sleep?" Twilight asked confused.

"You can sleep on my sofa I guess" Fluttershy said.

"But where will Rainbow sleep?"

"In my room" Fluttershy responded.

"But, wouldn't that be awkward? She doesn't have a sleeping bag"

"Nah it's cool, I've known Fluttershy for years"

"Well goodnight girls" Fluttershy bid her farewells and walked upstairs into her room and Rainbow followed.

"Who's gonna be the big spoon today Rainbow?"

"You, because you are bigger than me after all" Fluttershy smiled and held Rainbow in her hooves as the two drifted off to sleep.

Since that sleepover the four mares continued to hang out together as friends, however, little did they hear of Rarity and Applejack after what happened, Rainbow would sometimes see the two outside in public, they would share some awkward glances and hurry away from each other.
They simply grew distant after the argument and the friendship fell apart. Perhaps some things are best left unknown

Author's Note

This is my first ever story so I would appreciate some feedback.
Cover art by Mana95
https://mana95.deviantart.com/art/I-have-a-crush-on-you-Flutterdash-520091476