The Flightless Bird

by mckluv

Rating: everyone
Tags: Original Character, Rainbow Dash, Cutie Mark Crusaders, Maud Pie, Tragedy, Babs Seed, My Little Pony: Friendship is Magic, Dark, Sad
Length: 4315

5 years after Cloudsdale's destruction, a young pegasus spy finds her prey- but not how she wants it.

Waterfall Mist is a spy for the Master. Her prey is the Flightless Birds, a group that formed on stopping the Master and restoring Equestria. After finding the HQ, the leader of the Birds kidnaps Waterfall and brings her to a strange room.

What happens there is something she never expected.

Edit 11/22/18: I know this is incomplete. I honestly only realized that now... oops. I'm putting "Canceled" because I lost the Google Doc that I was writing this on. Double oops.

Published 2017-01-19 13:40:01 UTC
Last updated 2017-03-21 17:08:36 UTC

HQ

Hello.

A voice cut through the darkness. But how? I was alone.

I know why you’re here.

I started to sweat.

But don’t worry. I won’t hurt you.

I started to sweat even more as a shadow flitted across the window. I looked at the window, then back at where I had been.

Somepony was there. I screamed, but the young filly in front of me stuck her hoof on my muzzle. The hoof that silenced me was orange. I also saw a glimpse of a short purple mane.

“Who are you?” the filly asked me. I couldn’t answer.

“Mmph!” I pointed to her hoof.

“Oh, right.” She giggled, then removed her hoof. “Sorry. I just couldn’t have you screaming. There are… things out here.”

I stared at her. “What kind of things?” I asked. The filly shushed me.

“I’ll explain everything back at the HQ. I promise.”

The HQ was almost as big as the barn at Sweet Apple Acres. HUGE, I mean. The young filly led me through a giant maze, then another maze, then ANOTHER, but it seemed like she’d gone this way 100 times. We finally reached a room with only a lamp inside it. With some kind of magic, the lamp was lifted up and shone on the filly.

This filly did in fact have a purple mane and an orange coat, as well as purple eyes and tiny wings. As she walked over to me, a breeze ruffled her bangs. They slid aside to reveal- a horn?! It was pulsing magic. So this is how she’s lifting that lamp… I thought. What knowledge to get back to the Master!

As if she could read my mind, the filly snapped a device on my horn. “You’re not telling the Master any of this. This is top secret information. That door was supposed to be shut; I don’t know how a breeze got in here in the first place. My name is Commander Scootaloo, leader of the Flightless Birds. And I want you to join.”

I stared at her, then laughed. “I’m a unicorn, Scootaloo!”

She raised her eyebrows, then tore off my horn. I screamed, then she cut the bottom of my mane. My wings were revealed. I blushed.

She sat back down in her chair. “Why do you hide your wings?” she asked me. “I wouldn’t do that, even if I can’t fly.”

“You can’t fly?!” I couldn’t believe it. “But you’re the leader of the Flightless Birds… oh.” I had just figured it out. “That’s why you want me.”

She stared at me. Then she smiled. “That’s not why. Really. It’s because the Master isn’t who you think she is.”

“What are you talking about?!” I glared at her. “You wouldn’t know! You’ve never met the Master!”

“Yes I have!” Her response shocked me. “But before I tell you how, tell me your name.”

“I’m Waterfall.” I said. “Alright, now tell me your story!”

About 5 years ago…

“Rainbow Dash and I were best friends. We were inseperable! Until the day this war started, we hung out, had fun… she even tried to teach me how to fly!” Scootaloo sighed. “Those were good times.”

“But what happened?” I asked.

“There was a… problem in Cloudsdale. Even the Wonderbolts couldn’t fix it, and they could always fix stuff! When we found out THAT fact, Twilight told her friend Sunset Shimmer that a place called Canterlot High was about to get a lot more people, whatever those are, enrolling. Then she opened up a portal and evacuated almost all of Equestria!”

“Almost all? Why not all?” There was one problem with that explanation.

“Because 9 ponies stayed behind. Twilight didn’t know, nopony could! We had been trapped in the wreckage of Cloudsdale and-”

“The WRECKAGE?! But that’s where-” I shut up. I couldn’t reveal where the Master had been having her HQ for the past 5 years.

“We know. The Master has her HQ there. So you’re not spilling anything.” Scootaloo smiled at me. “The 5 leaders were there, along with Rainbow Dash and 3 others. Along with me, Sweetie Belle, Apple Bloom, Diamond Tiara, and Silver Spoon are the leaders of the Flightless Birds. Rainbow Dash, however, after we finished setting up this HQ in the ruined Ponyville Schoolhouse- we moved it after it got burned down 3 years ago- had disappeared, along with Maud Pie, Babs Seed, and, well…” She stopped.

“Me.” I knew it. “I was there, wasn’t I?” I stared accusingly at Scootaloo.

“Yes, you were,” she said. “I tried to bring you to our group, but Rainbow Dash flew you over the waterfall to the only part of Cloudsdale that hadn’t been destroyed. That’s how we knew where their HQ was, and it’s how you became the youngest pony to get her cutie mark!”

“What are you talking about?” I knew I got my cutie mark early, but being the youngest pony to get one was just inconceivable.

“You were the youngest pony to get your cutie mark! Your cutie mark is a waterfall with a cloud at the top, right?” Scootaloo’s wings flapped with excitement, but she soon floated back down.

“Um…” I looked at my cutie mark. It was! “Wait. How did you know?”

Scootaloo looked at me. “Because, when Rainbow Dash took you away, I tried to follow. I saw your cutie mark! It was awesome. I knew that you really had a chance to be here, for we don’t usually accept ponies without their cutie marks. It was sadly Diamond Tiara who made that rule, of course excluding us at the time because we were part of the leaders. Then, when she became our friend, we stopped trying to get our cutie marks and instead tried to help other ponies get theirs, we got ours, and we just never really found time to get rid of the no-blank-flanks rule. We just… well…”

I smiled at Scootaloo, and just as I was about to tell her something, Apple Bloom rushed in.

“Howdy, Scootaloo, howdy, Waterfall! Are ya havin’ fun? Ah sure am! Ah know that many ponies wouldn’t get it, but Ah know about this because ah spied on the Master!” Apple Bloom kind of looked like herself, but half of her looks like Pinkie Pie.

“Apple Bloom, what’s up with the Pinkie Pie look?” Scootaloo and I said at the same time.

"Is there something wrong? Are you okay?" Scootaloo asked, right after.

“Me? I'm fine, and nothing's wrong, 'cept for the fact that there's the Master right outside!”

Author's Note

Waterfall is my OC.
No stealing.

This takes place during the Fall of Equestria. If you want background info, here it is.

The Rainbow Factory explodes, and rainbows are EVERYWHERE. Ponies start finding filly bones in the rainbows (reference to rainbow factory) and that is the "problem."

Nopony wants to think that the rainbows that they love so much are actually ground-up pegasus fillies.

Return

Waterfall screamed.

“What the heck?!” Scootaloo looked at the Master, who was staring at Scootaloo as well.

“Scootaloo…” The Master’s eyes softened, and she hugged Scootaloo, who looked really confused. “It’s good to see you.” Then her eyes became cold. “Why did you filly nap my assistant?” Maud and Babs cowered behind her, shivering.

“We didn’t filly nap anypony!” Sweetie belle yelled. “That’s what YOU did! With Babs!”

“I did what I had to do!” The master stared at Sweetie Belle. Then with a speed that nopony could surpass, she swooped towards Waterfall and picked her up, causing her to shriek.

“Put her down!” Apple Bloom yelled, angry.

“Mwahaha! Hmm… let me think… NO.” Then the Master flew away, leaving the three fillies angry and confused.
*********************************************

“Ah can’t believe it! We finally get somepony to help us, and she’s stolen! This is great, just GREAT!” Apple Bloom fumed. Scootaloo, who was fiddling with the computer, didn’t answer, while Sweetie Belle put her hoof around Apple Bloom’s shoulder to comfort her. That’s when Scootaloo leaped up.

“That’s it! I’ve got it!” she yelled, startling the other two fillies.

“Got what?” Sweetie Belle asked.

“You remember that tracker on Waterfall’s tail? Well, I’ve tracked it to the Master’s hideout, which we know! Let’s go!” She started running, only to look back and see Apple Bloom and Sweetie Belle still in the other room, looking at her with sheepish looks.

“What?” Scootaloo asked them.

“Well, we’d love to go…” Apple Bloom started,

“...but I’m scared! And Apple Bloom’s gonna stay with me!” Sweetie Belle answered, hugging Apple Bloom’s leg. Scootaloo facehoofed.

“Fine! I’ll go by myself!” And with that, she jumped on her scooter and zoomed off towards the only remaining part of Cloudsdale, where the Master, and Scootaloo’s new friend, were waiting.

Author's Note

Will continue soon! :derpytongue2:

Factory

Scootaloo was one fast filly. Before the Incident, Scootaloo was THE fastest filly- the Ponyville Schoolhouse even had a race to prove it. But no amount of strength could get her to Cloudsdale. She hadn’t called the group “The Flightless Birds” for nothing, after all. Devising a plan, she grabbed her scooter, her wings flapping furiously, and started getting herself up there. She was halfway there when she dropped her scooter.

“No!” The scooter, now broken, was lying beneath her. She snorted. That scooter had been with her before the Incident, before her cutie mark, when she had first met her friends, and now, because she couldn’t reach a simple cloud, it was broken. While she was thinking, she got even angrier. Then, like they had a mind of their own, her wings started flapping. She was so angry she didn’t realize what she was doing until she did a 360° in the air.

“What the…” She looked down. She was ABOVE Cloudsdale. She was flying. Actually flying! Getting on the patio of the Weather Factory, she stopped to catch her breath. Then she realized something.

“Oh no. It’s fun flying, but I can’t be a member of the Flightless Birds if I can’t fly! That’s the whole point of the group! Nopony there can fly and it’s a place to do two things: help flightless pegasi like me 2 minutes ago be accepted, and also to help other fillies find their place! Well, I guess to spy on the Master’s group as well, but we don’t really do that often… Well fine! Who cares! If I have to leave, then saving Waterfall will be my last duty as a Leader of the Flightless Birds!” She smiled confidently to herself. Then she heard a scream from the Weather Factory.

“Waterfall!” Scootaloo kicked open the door. There was a crunch and the door flew off its hinges. Scootaloo chuckled to herself. That door’s been used last in the year who knows when, she thought to herself. No wonder it broke after one kick from a filly.

“Ah, Scootaloo. Nice to see you again! Don’t you remember this place?” A voice brought her out of her thoughts. “You were the one filly to escape. Don’t tell me you forgot!” It was the Master. As Scootaloo looked around, she noticed that it was familiar. The conveyors… the stench… the color… everything. The Rainbow Factory.

“But I thought it exploded!” Scootaloo yelled, truly scared now. Apple Bloom and Sweetie Belle had the right idea… I hope they’re okay, whatever they’re doing. She remembered that when she had failed her flight test, two pegasus stallions had brought her and her new friend Orion to this place, along with a young filly named Aurora Dawn. When that filly had been shoved down the Pegasus Device, Scootaloo had kicked a guard, causing him to scream and use words that fillies should not be hearing. He had grabbed for her, but by then she kicked a hole in the cloud floor and tried to fly down. She ended up falling into Ponyville. By then she met Sweetie Belle, and when she met Apple Bloom at Diamond Tiara’s cute-ciñera the Cutie Mark Crusaders were born. And Rainbow Dash had finished her evil ways and ended up letting Scootaloo be under her wing and taught her flight tips, hung out, and, well, taught the filly to be totally awesome. Rainbow Dash was the ultimate sister. Or so Scootaloo thought. “Why are you doing this? I thought you had finished being evil after I escaped!”

“Really? You actually thought I wanted to let you under my wing? I was actually NOT letting you out of my SIGHT!” Rainbow Dash was angry.

“Remember your friend Orion? Well, I let him live. He works for us now. Come on out, Orion. Say hi to your old friend.” A shape came out of the darkness. It was Orion.

“I don’t have any friends.” The words stung Scootaloo like a knife. “The one friend I had abandoned me. Why would she be my friend now?”

“Orion, I wanted to bring you with me. Really! But you were already above the machine, being held by Rainbow Dash. I couldn’t save you without possibly being killed myself. Orion… please…” Scootaloo held a pleading gaze on Orion. “Please…” He looked confused.

“You want my help?” Orion asked. Scootaloo nodded. He held out a hoof to her. “Take it, I’ll make sure they let you live,” he said. Scootaloo reached for his hoof and grabbed it. That’s when Orion pushed her toward two burly pegasus guards. As they grabbed her, Scootaloo felt like she was about to cry.

“Why would you do this?” she asked Orion, tears threatening to spill.

“Not all ponies are trustworthy.” Orion answered. “Take her away. Get her out of my sight.” And following their orders, the guards dragged a sobbing Scootaloo to the Rainbow Factory dungeons.

Author's Note

Note: Original Rainbow Factory fanfic is here.

Also, alternate universe to Rainbow Factory. In this universe, Scootaloo escapes the Rainbow Factory. Orion lives, but works at the Factory, and Aurora still dies.

Escape

“Good-bye, Scootaloo. You were a great filly. I actually really liked you… Sadly, you messed with the wrong pony. I’m always 20 percent cooler. 20 percent awesomer. And 20 percent normal!” Rainbow Dash laughed horribly. She turned on the Pegasus Device. It started whirring. That’s when the guards brought in Scootaloo and Button, knocked out. As one guard tied Button to a chair, Scootaloo started to wake up.

“Rai… rainbow Dash? Wha...what’s going on?” Scootaloo asked.

“I’m about to kill you, you worthless filly! You should look a little bit more scared…” Rainbow Dash muttered that last part. “I don’t know what’s worse: being you right now, or being around you right now!”

*******************************************************************

Meanwhile, Apple Bloom and Sweetie Belle were right outside the ladder that lead to Cloudsdale.

“Are you sure that this’ll work? Ah’m not sure about this…” Apple Bloom said, looking at Sweetie Belle. “Scootaloo’s fine. She said so herself!”

“Yeah, no. When Scootaloo gets determined, she usually does it with no thought to the danger, which usually means she gets in trouble. We have to help!” Sweetie Belle glared at Apple Bloom. “Come on!” She kicked down the door. Well, she expected to, but the door was already off, causing Sweetie Belle to flip over and land in the middle of the Weather Factory. A surprised Rainbow Dash, an equally shocked Button Mash, and an also equally shocked Scootaloo stared at her.

“Well, well, well, another filly? We have 2 fillies to kill today, huh?” Rainbow Dash laughed evilly. She stepped forward to grab Sweetie Belle, but she was knocked off balance by Button Mash, who had escaped the guards and had jumped on her. As Apple Bloom untied Scootaloo, Sweetie Belle and Button Mash avoided Rainbow Dash’s guards, and Rainbow Dash screamed for more guards, everything suddenly ended in a cloud of smoke. Everyone started coughing, and in the confusion the three fillies escaped into the night. When the smoke cleared, Rainbow Dash shook her head. “Alright, Scootaloo and her friends, prepare to- die?” She stared. Scootaloo and her friends were gone.

Author's Note

It looked longer on my Google Doc...

Enjoy it :pinkiesmile:

Elements

“Good-bye, Scootaloo. You were a great filly. I actually really liked you… Sadly, you messed with the wrong pony. I’m always 20 percent cooler. 20 percent awesomer. And 20 percent normal!” Rainbow Dash laughed horribly. She turned on the Pegasus Device. It started whirring. That’s when the guards brought in Scootaloo and Button, knocked out. As one guard tied Button to a chair, Scootaloo started to wake up.

“Rai… rainbow Dash? Wha...what’s going on?” Scootaloo asked.

“I’m about to kill you, you worthless filly! You should look a little bit more scared…” Rainbow Dash muttered that last part. “I don’t know what’s worse: being you right now, or being around you right now!”

*******************************************************************

Meanwhile, Apple Bloom and Sweetie Belle were right outside the ladder that lead to Cloudsdale.

“Are you sure that this’ll work? Ah’m not sure about this…” Apple Bloom said, looking at Sweetie Belle. “Scootaloo’s fine. She said so herself!”

“Yeah, no. When Scootaloo gets determined, she usually does it with no thought to the danger, which usually means she gets in trouble. We have to help!” Sweetie Belle glared at Apple Bloom. “Come on!” She kicked down the door. Well, she expected to, but the door was already off, causing Sweetie Belle to flip over and land in the middle of the abandoned Rainbow Factory. A surprised Rainbow Dash, an equally shocked Button Mash, and an also equally shocked Scootaloo stared at her.

“Well, well, well, another filly? We have 2 fillies to kill today, huh?” Rainbow Dash laughed evilly. She stepped forward to grab Sweetie Belle, but she was knocked off balance by Button Mash, who had escaped the guards and had jumped on her. As Apple Bloom (who had gotten in while everypony was distracted) untied Scootaloo, Sweetie Belle and Button Mash avoided Rainbow Dash’s guards, the now-untied Scootaloo grabbed Waterfall, and Rainbow Dash screamed for more guards, everything suddenly ended in a cloud of smoke. Everyone started coughing, and in the confusion the five fillies escaped into the night. When the smoke cleared, Rainbow Dash shook her head. “Alright, Scootaloo and her friends, prepare to- die?” She stared. Scootaloo and her friends were gone.
*****************************************************************************************

“Phew!” Scootaloo sighed. “I will never get used to that place.” The 5 fillies- Scootaloo, Sweetie Belle, Button Mash, Apple Bloom, and Waterfall- were finally back on the ground, looking up at the sky for a glimpse of Rainbow Dash or any of her guards. There was no sign of any guards or cyan pegasi. The Rainbow Factory, however, was shaking violently, so they watched the Factory as well. Then there was an explosion from inside.

“What… was THAT?” Apple Bloom asked. As she spoke, the Factory was shaking even more than before. Then, Rainbow Dash flew out of it.

“There they are! Get them!” she cried. The fillies screamed. As the Rainbow Factory guards flew out as well, the shaking stopped. Everything was still. Then the Factory started plummeting to the ground. Seeing that the sky had suddenly gone dark, Rainbow Dash and her guards took their eyes off of the fleeing fillies for a second to look up at the sky.

The sky was gone. In its place was the falling Rainbow Factory.

Now, everypony knows that clouds are fluffy and soft, and that they can’t hurt anypony at all. But there was a dangerous object in those clouds, which was very heavy, and which was also upside down, and it was right above Rainbow Dash.

So as Rainbow Dash tried to fly away, the Rainbow Factory fell on her. She popped her head through the clouds, only to find her own filly-killing invention land on her.

“NOOOOOOOOOOOOOOOO!!!!!” Rainbow Dash yelled, screaming in fright. The guards looked on in horror, their loyalty to their leader clashing with their want to stay alive. There was the sound of sawing, blood spurting, and finally the *GAK* of a pony being choked to death. To end it all, a beautiful rainbow flew over the sky.

Scootaloo started crying. “Don’t worry, Scootaloo,” said Waterfall. “It will be okay. She tried to kill you, remember?”

“Yeah!” added Apple Bloom. “You almost died. Isn’t it good that she’s dead instead of you? I know that she was special to you-”

“Special?!” Scootaloo jumped up in anger. “She was my sister! Well, a pony who took care of me like a sister!”

“She also tried to destroy Cloudsdale, all of Equestria, and all the fillies who live there!” Sweetie Belle retorted, annoyed. “Why can’t you look past the good? Maybe now Twilight and her friends can come back with the rest of Equestria and reinhabit it!”

“Yeah, maybe…” Scootaloo thought for a minute. Then she gasped. “But without the Element of Loyalty, who will save Equestria?”

That’s when Apple Bloom smiled. “Babs has a little plan with that in mind,” she said, smiling big. “My cousin wasn’t always evil, you know!”

Babs Seed and Maud Pie, who had survived the explosion, walked up to us. Babs, with the help of Diamond Tiara and Silver Spoon (they had heard the explosion from the Flightless Birds HQ and came to see if anypony was hurt,) laid out a piece of yellowing paper. Seeing our expressions, she quickly explained why. “The Master- I’m sorry, Rainbow Dash- never really used paper. I saved this from the wreckage of your first HQ, and I used it to create a plan if Rainbow ever died or got to old to rule our crew.”

“Hey, wait a minute!” Sweetie Belle levitated the paper with her magic and turned it over. “That’s mine! I wrote a song right before the Ponyville Schoolhouse burned down so that I could remember it!” Apple Bloom stared at her. “Rarity used to sing it to me before the Incident.” Sweetie Belle replied defensively.

“Anyway,” Babs said, trying to get back on track. Taking the paper back from Sweetie Belle, she continued: “I think that it’s possible for new ponies to wield the Elements.”

“What?!” The 8 other ponies stared at Babs, shocked with the news.

“I’m just saying…” Babs suddenly turned around. There, hidden in the rubble of the Rainbow Factory, was a book. Babs smiled. “I knew that it would be safe!” She ran over to the book and picked it up. Flipping to a certain page, she showed us the words on them. However, there were no words. Just 6 gems… 6 gems that had saved Equestria from countless problems. “This book is called The Elements of Harmony: A Reference Guide. During Discord’s return, he hid the Elements of Harmony in this book. Luckily, he never removed the pages they were hidden in. When the Incident happened, Twilight placed the Elements in the book so that they couldn’t be used for evil in the other world. Apparently that had happened before. She meant to come back, but during something called the Friendship Games the portal got closed and by the time it reopened, they were fighting a magical creature that was hell-bent on destroying their world. It could even tear portals out of thin air!”

“So that’s how a hole appeared out of thin air in the sky,” Scootaloo said, now wanting to kick the creature’s butt. “Thanks to that thing, I threw up for a week!”

“Why?” asked Sweetie Belle.

“Because I saw something that looked exactly like me. ‘Cept it walked on two legs and wore clothes.” Scootaloo shuddered.

“ANYway,” Babs said, giving Sweetie Belle and Scootaloo a death glare, “they’re right here, with nopony to use them. Who wants to try them first?”

Author's Note

Note: I don't actually want Rainbow Dash to die.

Also, only 2 chapters left until the end! :)

Might write a sequel, but only if you want me to! :derpytongue2:

Masters

“WHAT?!” Scootaloo and I freaked out. “The Master is here?!” Closing the shutters, the three of us grabbed boxes and hid behind them. Before long, there was a knock on the door.

“Hello?” A voice sounded from outside. It was Babs Seed. “Is anypony in there? We would’ve come sooner, but we just found out your new HQ’s location! You do know it was us who burned down the Ponyville Schoolhouse, right? I was there. I lit two of the matches!” She sounded giddy. “It’s great that you have a new place. I just think-” She was cut off.

“Calm down, Babs.” A new voice sounded. It sounded familiar… almost like… the Master? What in Equestria was she doing here? “Come on out, Scootaloo. Don’t think we had a choice. The tracker worked perfectly. Good work, Waterfall.” She laughed. Tracker? What tracker? Then I looked at my tail. Along with the hot pink barrettes I place in my tail every morning, there was a barrette that was flashing a neon blue light. I gasped. Scootaloo and Apple Bloom, along with Sweetie Belle, who had come in to see what was going on, stared at it.

“You led her to us?!” Apple Bloom glared at me. “Once a spy, always a spy. Scootaloo, kick her out. The Master’s outside, she’ll take her back.”

“I didn’t know she placed a tracker on me! Honest! Apple Bloom, as the sister of the Element of Honesty, you should know! Please don’t kick me out!” Then I whispered in Scootaloo’s ear, “I actually want to join your group now. Now that I know what happened…”

Scootaloo blinked. “You… want… to join us?” It looked like she couldn’t believe it. Apple Bloom and Sweetie Belle looked at me. Then they smiled.

“YAY! The Flightless Birds new member!”

Then there was an explosion. The door crashed to the ground. And there stood the Master.