The Future of the Wonderbolts

by Megaskullmon

Rating: mature
Tags: Queen Chrysalis, Scootaloo, Adventure, Princess Celestia, Crossover, Gore, My Little Pony: Friendship is Magic, Alternate Universe, Main 6, Princess Luna, Drama
Length: 7060

The old Wonderbolts retire a compleatly new team is formed.

It's been 30 year's Since Scoots has been able to fly. The older wonderbolts are starting to retire. But down the line Equestria has made some advancement's. Can the Wonderbolts stay as the main part of the Military in a new peaceful world? They start to learn that the Wonderbolts may be shut down..Because of the Advancement's and Rainbow Dash vanished suddenly.

To find her they must convince the old wonderbolt's to take to the sky to find her.

Take's place in the same Universe as Project Harmony.

http://www.fimfiction.net/story/274800/project-harmony-one

Published 2020-06-05 00:30:02 UTC
Last updated 2021-08-09 22:42:33 UTC

Chapter one: Letter From Rainbow Dash.

"History starts with a cry... Not with a bang... The bang is the gun in your hand."

Present

The letter goes on.

"I wished I could have told you what I was going to do... But I couldn't Maybe someday you will forgive me... I can't believe how it all started.

_______________
Two thousand years ago.

It was a calm peaceful morning in Ponyville. The outside was calm and gentle. Inside Scootaloo's home, she was in her bed, sleeping near her husband, an earth pony and she married him soon after she got in the reserves.

Scootaloo woke up in her bed. She woke up near her husband. She looks to the earth pony with a gentle smile and kisses him on his cheek. She went downstairs, her foals were not awake yet. As she looked through the mail, she finds a letter from Rainbow Dash. It said on the front of it that the letter was urgent.

She opens the letter and starts to read. {Scoots, I need to speak to you, it is urgent. I need you to fly to the Everfree forest. We will meet at the castle of Two sisters. Also please rip up this letter. Don't let Half Note read it or your kids.} She blinks and rips the letter up and tosses it in a new advancement for trash. A magic trash can that..turns stuff to ash.

She leaves a letter for her family. {I am heading to the store for some food and milk. I will be back in a few hours. Half Note, make sure the kids do their homework.} She places it on the fridge and heads outside. She looked up seeing the new advancements. Seeing the first model of robots and some flying cars... She wondered how quickly the world changed.

She flapped her wings and soared into the air and flew towards the Everfree forest. She looked to see a rocket ship being built... It was said that it won't be leaving Equestria for maybe a thousand years or more. She flew into the castle and she wasn't alone. As she landed, she saw Flashfly, the daughter of Spitfire. She then saw Nimbus, the son of Sorian, and also saw Cloud Skipper, the daughter of Cloudchaser, and then saw Winghoof, the daughter of Fleetfoot. They all looked like their parents. Flashfly looked so much like Spitfire.

They all look to Scoots. "You got a letter too?" Nimbus calmly asked. He seemed shy. He was the youngest of the group.

Flashfly looked the youngest but..she acted very maturely for her age. She snorted and looked around. She had her mother’s sunglasses on. "I don't know why we are here..."

Then, a voice rings out. "Wonderbolts, in line!" Out of the shadows comes Rainbow Dash and she stared at them all as they got in line.
"What I am going to tell you ponies, is this... Your parents have fully retired from the force... I want you to take over for them." They blink and have smiles on their faces. She walks to Flashfly "You will be the first in command." She looks at Scoots. "You're second... You know the rest... Now, with the advancements in our world... The Wonderbolts are being slowly removed from the daily lives of Equestria... We need to try to prove that we are better than that.."

They all salute and go. "YES SIR!"

Rainbow smirks and then chuckles. "I want you all to be at the camp in the morning. I will be there to tell you about your orders. Then you're on your own."

Twilight flew into the castle. "So... I see we have new Wonderbolts." Twilight smiles and goes over to Rainbow Dash giving her tight hug.

"Wonderbolts dismissed." They all nod and fly off but Scootaloo stayed put.

"I am getting married Rainbow." Twilight smiles happily.

Rainbow gives her a look sighing. "You know I don't trust...the guy...but if he loves you then I can try to trust him." Twilight smiles and hugs her friend. Amazingly after 30 years, she is growing in size. She is taller than Rainbow but she still considers them her best friends.

"Also we kind of have to get married..." A blush started to form on her face and Rainbow gets very upset and angry.

"He did that to you?!" She then calms down and sighs and looks at Twilight. "You're a Princess, it's going to be rare for you to find someone. With the death of Flash, I guess he is the only one that took interest in you." Twi nodded.

"Anyway," She blinks looking to Scoots and smiles. Scoots blinked and gulped a bit, looking worried. Twilight walks up to her and wraps her forelegs around Scoots, hugging her tightly.

"Oh, so good to see you, Scoots..." She smiles and gives Twi a tight hug and chuckles. "How are Half Note and the kids?"

"They're good. I do need to get some food and milk. Other than that, everything is doing great."

Twi smiles and nuzzles her. "How is CMC?"

Scoots blinked and looked down. "I haven't talked to them since Sweetie Belle left to do her singing. I haven't seen Apple Bloom either since she went to go live with Zecroa to learn potion-making. But I am sure we will meet again. They're both married... Apple Bloom married a Zebra. Sweetie Belle, of course, got married to a rich colt."

Twilight gives Scoots another tight hug and chuckles. "Well, good on them. I need to get back to my husband to be." She flew off as Scootaloo sighed and looked back to Rainbow Dash.

"I want you to be at the camp this afternoon. But go do your shopping." Scoots just rushed in and hugged Rainbow. She blinked and hugged her tightly, wrapping her wings around her. The two hugged for a while before she pulled back, smiling.

"See you later sister." Scoots flys off and Dash sighs, looking down.

Celestia comes out of the darkness behind Rainbow. "I know...that was hard for you Rainbow and to lie to your friend...this stallion I am sure is the one kidnapping ponies and giving them to the changelings. I can't tell Twilight this...because she would not buy it without proof. You do know...you might not live through doing what I ask."

Rainbow looked up to Celestia. "I agree...also the alliance hasn't been made public yet... So I need to get going soon and be ready to spy."

Celestia nodded. "If you get trapped there Rainbow, I can't come and save you... So you're on your own."

Dash nods and flies off as Luna comes up behind Celestia and she looks to her sister with a gentle smile. "Sister... I don't think this is wise...to do this... Twilight may turn on her friends...because of Dash doing this." Celestia hugged her little sister and nodded.

"I understand perfectly what is at stake dear sister... But we have to do it... The world is changing and many will not trust the Changelings and some don't even trust Throaxes group of Changelings. But Starlight will be there as well. I don't trust the fact that Starlight is going... But I hope she will be alright."

___________
A few hours later

Scootaloo makes it home and when she goes in, the house is ransacked, there is blood on the floor and her children are gone... But she drops the bags and notices Half Note on the floor, his love sucked out of him, he looks like a husk. She rushes to him and tries to wake him up. She has tears streaming down her face as she held him, yelling his name. Somepony from next door heard the crying and a mare rushed in and she gasped.

She trotted out and called for the guards. An hour later, nobody had ever seen a murder in this form in their entire lives. The mare known as Sweet Berry held Scoots tightly and nuzzled her as she sobbed.

Rainbow came to see why scoots didn't come to the Wonderbolt camp and Twilight was also with her and they saw her crying.

"Scoots...what’s wrong?" Twilight asked as she looked inside and gasped, putting a hoof to her mouth with so much sadness forming inside of her. Rainbow looked in as well and saw the state that Half Note was in. She grew angry, very angry. "Where are the kids?!"

Scoots cried harder and she tried to speak. "G..one...kidnapped..."

Rainbow eyes were full of anger as she looked to Twilight and stared at her. She pulled her into the house away from the other ponies and gave her the 5th degree.

"You still want to ally with the changelings? Huh?! DO YOU?!" She was very pissed off.

Twi stared at Rainbow, her anger coming back at her. "How dare you think it was the Changelings! I want to make peace with them, Dash... The ones I have spoken to would never do this."

Dash grew angrier and she wasn't afraid to show it. "You're sending Starlight there... I know this well, Twilight...you need to have more protection for her..." Twilight's features on her face and her behavior of movement show that she doesn't care.

"She will be fine... You need to trust me Dash."

Dash just stares at her and growls. "I do... Twilight."

She walks out with so much anger in her features, her wings folded to her side and looks at Half Note... She introduced him to Scootaloo. Now she must watch her little sister cry. She walked over and smiled at Sweet Berry.

"Please go home Sweet Berry, I will take care of her." Sweet Berry was mute and she nodded with a smile, giving her another hug before she headed home. As Dash sat in front of Scootaloo, she wrapped her wings around her. "I am sorry Scoots... I wish I got here sooner."

Scoots spoke softly, shaking. "If I was...here, I would have been killed as well...I feel like it's fate."

Rainbow holds her tighter and nods. "Come...let's get to the camp and then I can explain to the rest of what is going on."

She looks back at the body. "May I please say goodbye to Half note?"

Dash nods and Scoots goes back to the body of her husband and wraps around him, sobbing hard.

__________________________
Wonderbolts camp.

Three hours later Scoots and Rainbow Dash land and they get in line as she shows up. "Now your orders. An Alliance is being formed with the changelings... It's staying hidden until it happens. But your orders are this... To stay here and get ready for training. I also will be going there to spy and to be a representative with Thorax and Starlight Glimmer and Trixie."

They look over to each other, blinking a moment.

"What happens if something comes up then, boss?" Flashfire asked.

"You stay here and do nothing.." She flies away and the others look at each other and all of them are very, very worried.

____________
Present

"Oh, Scoots, I knew I was wrong... I knew it... I got to the hive and met Starlight, Thorax, and the Great and Powerful Trixie."

Spike was still in space as he looks to the old photo of the mane six and holds it close to his chest. "Oh... Dash, if you only knew...the future.

Chapter 2: Starlight's fear.

" A fear will happen if you allow it to happen."

______________
Present

The letter goes on.

" I didn't understand it then. But I do now. I know why Twilight wished to have this Alliance. That husband of her's she wanted to please him. He did something...Something so awful. I hope when you read this. You will learn why I did what I did. Please when you learn Scoots don't hate me. I love you, little sister."

Spike sighed closing his eyes as he slept the flight was going to take a while for him to get back to the station.

________________________
2000 years ago. Changeling Hives.

Starlight hasn't been back to Ponyville for the last 30 year's She learned everything she could from Twilight and went back to her old home. To lead it as she should have at the start. She is now the ambassador for Twilight when Twilight can't do it. She went back to the old Hive that she saved Twilight and her friends the last time so long ago. On the outskirts, she met with Thorax and his changelings. Trixie was there as well. She hasn't seen her for a long time. Giving her a tight hug.

With her age, Trixie has calmed herself and no longer wishes to boast. She still lives in that wagon that she brought with her.

" Hello Starlight...I have been here awhile talking to Thorax. He is unsure about this Alliance that Twilight wants. But they want us to wait for a few hours before we go." Starlight nods and watches as Rainbow fly by and head into the hive

" It seems Twlight's spy is here."

________________________
Changeling Hive

Rainbow Landed in the hive and a black-formed changeling came up to her and bowed.

" I see you are here. Come come." Rainbow Nods and follows as she is lead to the meeting room and looks at the room

" Hmm enough for all of them good."

Rainbow Said calmly and the Changeling smiles nodding.

" May I have a look around?"

The Changeling nods.

Rainbow nods and left the room when she leaves a pony walks in he had interesting Blue Eyes and he walked in with the Queen of the Changelings herself. Rainbow stayed by the door to listen.

" I am called.... war. I am part of an army called Disharmony. They are all over this world...They waiting for their time to gain a foothold. But first this meeting of an Alliance. Go along with it. Then after that. I will give you your reward Chrysalis. I will make sure you are on the front lines with our troops."

The queen smiles and laughs.

" Hmm sounds wonderful. What about those so-called Changelings."

War chuckles.

" First kill them after the Alliance is written. Then kill them. Then kidnap and kill Twilight and then take her place." The queen blinks.

" You aren’t her loving husband?”

He laughs softly and shakes his head.

" She may be holding my young. A mix of Disharmony and pony. I might let her live to keep the little one alive..till she gives birth and then kills her. Then have you transform into her. But we shall see." He smirks.

Rainbow Gasped softly and turns and Changeling smashes into her face and she is knocked out. Then she is dragged back in.

" My Queen....we have a spy." The Queen smiles and looks over Rainbow Dash.

" Hmmm, I see take her place..and warn the Wonderbolts that something bad is about to happen here. But don't do it till I tell you to."

War looks up to the Queen.

" Hmm what is your plan?"

The Queen laughs softly.

" To hit many stones...First...have Rainbow lure the wonderbolts into a trap and we kill them. Then we kill those fake changelings. Along with the Ambassador and then we let the wonder boots swoop in and think their saving them destroy them all to weaken the power of Celestia."

War smirks and leaves the room.

" I don't trust him..my queen..."

One of the guards says as he is guarding the queen.

" I don't either...But after all, this is said and done...We shall take him down as well. Then maybe I will have enough power to finally do my plans."

Rainbow Dash is dragged to another room by one of the Changelings and locked in another room. She seems out of it for now.

" Now... let’s allow them to talk and finally I can have my revenge. But that would be too easy..Going to do it slow and calm and then strike. Besides you need to pretend that I wasn't here." She walks out of the room and one Changeling transforms into Rainbow Dash. As they smile at each other and send out the representative of the Changelings.

____________________________
Outside the hive.

Starlight seemed a bit worried her eyes studied every part of the area hoping nothing goes wrong. She paced trying not to stress out as Trixie watches her friend with a chuckle and shakes her head. " Starlight...relax...Remember what I told you back in the hive so many years ago. You're very good at this stuff." Starlight looks to Trixie and smiles. Giving her a tight hug and nods.

" Thank you, Trixie." She hugs her again and Trixie smiles.

" Hey, I am telling you the truth Starlight. You're very good at it..don't let anypony tell you any different." Starlight smiles and gives her friend another Hug as they have gotten closer since they left each other's company for a couple of years but kept writing to each other. The representative landed in front of them and he smiled.

" Sorry for the wait. Rainbow had to make sure everything was ready and set up. I am very sorry." Thorax nods he flys off with the rest of his group of Changelings and flies into the hive. Starlight and Starlight get close and she closes her eyes as Starlight transports them right into the hive.

__________________
The hive meeting Room.

Thorax and his changelings wait in the room while Starlight and Trixie walk into the room as well seeing Rainbow Dash and they smile at her. As the Changling representative sits at the table with Starlight and the rest.

" Now let’s talk about this Alliance."

Starlight nods as she leans in the chair relaxing.

" Twilight wants both of you kind's to become one again and work together as one. But I know that won't be very easy to the point of it. It's to make sure that we work together for the future. Because we can't stop what is coming no matter how much we want to. Soon we will be going to space and maybe even but the thing is. We need to stop ourselves from having these issues and work together to bring a better future for the foals and so on for the future. What do you think?"

The changeling smiles.

" I agree I fully agree. I feel it's wise. " The changelings set down cups for all the changelings and Starlight to drink. As he lifts his own drink

" How about we drink to it." Starlight took a drink. The changeling smiled as he drank the same with Trixie. The representative stood up.

" Now now Thorax your changelings come with me. So we can speak. Allow the two ponies here to enjoy their drinks." Starlight nodded. Thorax followed the Representative along with others from his race

_______________
Top of the shattered hive.

Thorax hasn't been here for so long. He looked around seeing the rest of his kind with him. This is where they defeated the Queen...

" Now...we can do what needs to be done." The changeling representative nodded to Throax and around them they get surrounded by many Changelings and by surprise they try to fight back but after a while, every single one but Thorax is killed Thorax watches as his own changelings are killed in front of him...He tried to use his magic. But the drink. He was given...his magic is blocked. He even tried to fly but had no luck.

" Allow me...to take care of this traitor." Thorax stared in fear at his former Queen. Queen Chrysalis. She stood there and used her magic to lift him staring at him.

" You and that Pony Starlight Glimmer are going to know my revenge." She lifts him in the air and forces him down hard onto the ground crushing him and then tosses him off the edge his body landing with a thud. After he hit. Thorax dies quickly. " Hmm to quick for a traitor. I shall go find Starlight..and have my Revenge." The Changeling nods.

____________
Back inside Starlight was talking with Trixie and then suddenly the door swing open. Starlight Jumps up seeing Chrysalis and Trixie get on her hooves and stands in front of Starlight.

" Run...Starlight...we all know she is after you.." Starlight nods and runs out of the room to try to escape. Back in the room, Trixie's horn glows. It seems the drink didn't affect her and Starlight.

" Hmm, you think you can beat me a little unicorn?" Chrysalis calmly walks over seeming like nothing is going to affect her. Trixie uses her magic to hit the queen even though it hits her. It doesn’t seem to phase her. She picks up the table with her magic and tries to smash it into Chrysalis and it effected her somewhat...Her eyes glowing brightly know she is going to win this battle.

" Twilight will know...that you failed to protect Starlight." Trixie is backed into a corner she tries charging after her but she is lifted in the queen's magic and tossed into a wall her back legs cracking broken not able to run..She tries to get up but can't.

Outside the room, Starlight saw the shadow of what is going on. She saw the hoof of Chrysalis step on the mare and then bite into her Trixie screaming in pain and then nothing. A voice spoke out.

" Come...little Starlight... let’s not keep my revenge waiting Starlight started to run the Changelings letting her run. They look at her with sadness in their eyes. She runs outside and finds Thoraxes body dead...She has tears fall down her face. Seeing Twilight.

" Twilight go back!!" Twilight stands there.

" Why Starlight?" She looks to that pony male that she has been with for many years now.

" I think Twilight wishes to speak to changelings." Twilight Nods.

" Yes, I do.." She sounds very different like she is not fully there

" Twilight!!" She tries to shake her and she vanished...

" Twilight...." She looks to the pony male who has those blue eyes..she would never forget and behind her comes up the Queen.

" Twilight...is not here...you silly unicorn...but her husband is...As well as his minions."

She blinks seeing strange dark creatures show up around him. Dark evil beings. She feels so much disharmony being near them...Backing up right into the Queen. She turns to see the Queen and looks to the pony. She never got his name..he just appeared one day. Saying that he and Twilight have been married for 20 years. But she never met him till a year ago.

" Now...for my revenge..."

Starlight didn't know what to do. She just looked around in fear her eyes full of it. " We can...speak about this..I.." She was old now the wisdom of friendship filled her. Since the time of the Shadows they fought has she seen a threat. The army of Disharmony so fast. War smiles darkly showing his teeth.

" Now now. Friendship won't work anymore little unicorn. Twilight is being controlled to do things. To ruin this world to make it ready for our coming. But sadly you won't be around to see it. Will she Twilight?" The Twilight vanished that spoke to her replacing with another of the leaders of DIsharmony. Yanari the element of Dispare but in the form of a pony

" Now....break her..." Yanari said. Chrysalis lifted a rock smashing hard into Starlight's skull. A flash of her cyborg face part of her face. Then she breaks her body. Flashes to parts of her as a cyborg. After this is done she leaves the body laughing.

" I will leave her to die.." Chrysalis went back to her former kingdom on the hunt for Rainbow Dash.

" War.. are we willing going to just simply help her?" War nodded.

"We will Let the Wonder Bolts come to the Rescue. Let them be killed in the fight. Then kill that Queen and allow Rainbow Dash to be blamed. My wife to be will do what she should break the harmony of this world." He said laughing. " Also we must allow them to find that object in space. It might be useful to us. Now that the alliance is weakened we start weakening the door of Tartarus more. Come along."

Starlight lay there broken, and dying she fell into a deep Coma. Her two friend's dead because of her weakness Trixie Thorax his hive...

Chapter: 3 The future [Lead into Project Harmony one.]

The wonderbolts and the younger Wonderbolts along with Scootaloo are taking off their uniforms since their day of training is over. Scoots didn’t go very far she sat there like she was worried about Rainbow Dash. She hasn’t come back yet like she said she would be returning.

The younger wonderbolts felt the same way but they didn’t want to argue with Spitfire. It didn’t take very long but Twilight storms into the locker room. Everypony looks at her they have a worried look on their eyes.

“Princess, what has happened?”

Spitfire didn’t wait to ask she stood up her yellow fur glowing from the sweat. She just took her hood off from her wonder bolt suit. Twilight took a while to speak she is painting hard from the overworking of her wings. They twitch in pain from the overworking.

“I got word that the talks failed. I haven’t been able to contact Rainbow Dash or Starlight.”

The older wonderbolts put back on their outfits as the others get ready and Spitfire turns to them.

“You newbies stay here. We need guards to protect the base just in case we bring problems back with us.”

The newbies wanted to argue but they weren’t allowed to. Twilight turns her head to look at Scootaloo she walks over to her and pulls her into a secluded area.

“I can’t.”

Twilight groans like she is trying to warn Scootaloo about something like something is controlling her from speaking up. Scoots didn’t worry too much about it but she tilts her head wondering what Twilight is trying to say.

“Scootaloo go to Ember, please. Ask her if what I asked her and her dragons to build is ready. Please….”

Scootaloo was confused she nods putting her hood on and with Twilights magic she was able to sneak out without the others seeing her even the older wonderbolts didn’t see her leave. She quickly makes sure to get some food and water before leaving. She looks back at the base having a feeling in the pit of her stomach that it wouldn’t be there when she returns.

A few hours go by and Scoots took many times to rest on her way to the Dragon lands. The tension between species has gotten worse since that object has shown up in space. Ever since the alliance has been formed to protect the gates ever since the death of Cerberus. When Scootaloo lands there aren’t many dragons at all but just Ember alone.

“I was expecting Twilight. But I am sure she sent you to ask me if what we have been working on is ready.”

Scoots took a while to answer she quickly answers after a while.

“Yes, she wanted me to see if whatever you two were working on is ready.”

Ember nods her eyes shifting from normal to pinpricks a second. She strokes her head with her claws unsure what to think. Looking at the devices she pulls a crystal rock. Coming out of a strange electronic crystal ground are strange pods. There are close to ten of them one of them is already in use. Scoots walk up to the one in use and strokes the frost away staring at the mare.

“Sunset Shimmer?”

Ember nods quickly looking at the pods.

“Yes, Twilight calls it magic stasis and she has been working on it ever since she helped form the alliance and ever since she met this pony called War. She told me many things that sounded crazy because of this pony. That he is from a race called disharmony that he controls her when he is close to her. I have been thinking she is crazy but I have been told things by others including Discord the balance of harmony is dying. Why the dragons have gone into hiding till the time is right.”

Scoots took a deep breath nodding.

“She has a pod inside the stairs of her castle I don’t know why these were created. But please just give her a nod and don’t tell her how many.”

Scoots turn around to fly and she looks back to Ember.

“After my family was killed not too long ago. I have started having a feeling that something awful was going on. These stories are starting to bring into place what I have been worrying about. Twilight and the other princess aren’t all-knowing like they say they are. I have known Twilight for many years. I never even fell for that fact with her. The others thought if they knew everything. Why are they scared of an object we can’t even get to?”

Ember thought of this a moment and quickly nodded agreeing with Scoots on this matter. Scoots flap her wings and fly away from the dragon lands it took her again a few hours to get back and when she got back. The horror she saw made her stomach lurch almost making her sick.

On many stretchers are the bodies of dying or dead wonder bolts. A body bag with the cutiemark of Spitfire lays with the others while the older wonderbolts all seem but dead. The only one alive for the time being Fleetfoot with a missing wing.

Scoots watch as the body of a living Starlight is carried through Twilighing vanishing with her mouthing something about a pod.

_____________________
Twilight castle.

Twilight finally gets back to her castle with Starlight’s body floating in her magic tears streaming down her face. She sobs loudly no one is even around but Starlight opens her eye staring at the weeping Twilight.

“Your husband to be. War is the cause of this. Please Twilight listen to me for once….”

Twilight silences Starlight her eyes shifting from their normal hue to a darker hue like she is fighting control. Whispers go deep into her mind.

“Kill her. Twilight she knows too much.”

A voice screams in her head she lays Starlight’s wounded body on the ground. She fights the voice of war in her head. She loves him or does she? She has no idea anymore who she loves. She groans and finally wins for now. She uses a spell to put the wounded Starlight asleep.

She opens the stairs in there a magic pod like the others that Scootaloo saw. Tears stream from her eyes as she writes a letter to Starlight.

‘Please forgive me someday Starlight. But I can’t rescue you and your soul now. When the time calls for it. I will wake you back up hoping that I can find a way to save you. I promise you I will never betray you.’

Many years from now Starlight is released and Twilight places cybernetic implants in Starlight to control her. The note sits near the pod-like Twilight never remembering that she wrote it. She promised she would never betray Starlight.

Back many years before the future. Twilight finishes the letter and looks down at her broken pupil. She closes her eyes more tears streaming from her face. She places the sleeping Starlight with the note into the pod.

After she closes the door locking it like it was never there. She turns to see the door open and her husband to be War walks into the room she shakes and shivers at his presence. She is unable to fight him.
“Twilight I heard the talks failed and then the Wonderbolts were lead into a trap.”

Twilight gulps trying hard to fight his control over her. She relaxes knowing he will never learn that Starlight is alive and in a pod. She took a deep breath and exhaled walking to her husband to be sitting beside him to listen.

“Go on.”

War didn’t take long to spread his lie.

“Rainbow Dash betrayed you and your friends. She then brought the Wonderbolts and set a trap just for them. You must do what you’re willing to do with the betrayed.”

Twilight didn’t want to listen but it didn’t take long for Twilight to send the guards despite how Celestia and Luna felt about it. Many days later the younger Wonderbolts come back from the funeral and when Scoots goes into the locker room first. Rainbow Dash pulls her in closing the and she hugs her little sister.

“Rainbow Dash?! What are you doing here they’re hunting you!!”

Rainbow quickly releases the hug. She opens the door and quickly turns to look at Scootaloo. She closes the door quickly. She then pants softly breathing normally after a second. She opens the door to call the others in.

“Before you speak and warn the guards I am here. I need you to do something for me. In the dragon lands, some pods have been made to protect you all. I can’t tell you why but. I trained you all and I am going to miss you all.”

Scootaloo looks at the others and they didn’t argue.

“I speak for all of us that I feel it’s wise for us to go to these pods.”

The group of the new Wonderbolts left Scootaloo turning to Rainbow Dash giving her a quick hug and sitting on a chair Rainbow Dash writes a note putting it into an envelope saying to Spike don’t open it till the time is right. She quickly finds a pigeon and with a trick that Fluttershy taught her years ago. She told the Pidgeon to take this to Spike.

Rainbow Dash sat there waiting for the guards to come for her. With her wings, she lifts a photograph of her and the other Wonderbolts. When she first became part of them. Tears fall from her eyes as she remembers everything.

The door opens up and standing some guards didn’t want to even go after Rainbow Dash they saved them so many times and they felt they had no right to go after her but they had a job to do. She got out of the seat and offers her hooves to be chained up.

Scootaloo looks into the window since she and the others haven’t left yet she wanted to fight the guards but she knew she shouldn’t. She flew with the others to the Dragon lands and Ember throws the lever and the pods came up she didn’t even say a word till she opened them up.

“I don’t know if these were created for you or not. But these will put you asleep and you will be here till the time is right to wake you.”

The other new Wonderbolts didn’t even speak most of them are still getting over that those above them died and they go inside each door closing Scoots was the last to go in. She turns to Ember and her eyes are full of tears.

“What has gone wrong Ember? Ever since Cerberus’s death and that thing showing up in space things have gotten worse.”

Ember shrugs her shoulders.

“I wish I could tell you. I wish I could tell you everything will be fine I can’t even see the future myself. Just good luck to you.”

Scootaloo goes into the pod and the door closes down and she watches the last thing she sees Ember waving to her as she falls into a deep-frozen sleep. Ember pulls the crystal rock again and the pods go back into the ground till the time to bring them out is needed again. She looks back at the dragon lands seeing more and more dragons going into the hiding.

Back in Cantorlot and many hours later Rainbow Dash is brought to the others and Twilight holds an ax beside her as she has fully changed and War stands right behind her. She uses her magic to hold the ax tightly to her side. Spike held one of the devices that came from the tech boom to get into space. He learned how to edit he called it a camera

“Rainbow Dash you’re accused of betraying the ponies and destroying the peace talks. You’re accused of the deaths of Thorax, Trixie, and Starlight. I will allow you to speak before I bring forth the judgment towards you.”

It took a while for Rainbow Dash to speak up.

“I never did such a thing. I was warned about War he is the cause of all this. You can’t see it yourself you’re blind!! You have known me all your life almost Twilight and you know I would never lie to you.”

Twilight took a while to answer she breathed deeply to try to relax and deep inside her mind she heard War speak to her again in her mind.

“Do you want to look weak to your friends my love? Do you also see that thing Spike is using? I would like you to force him to edit and make her look like a threat the best way you can of course.”

He smirks

“I am sorry Rainbow Dash but I curse your entire family name. I will hunt down all your family till I find one that will never betray me again. This curse will only be broken when a Dash finds me if I haven’t destroyed them all and fight me for revenge.”

It didn’t take long for Twilight to lift the ax tears streaming down her face. As she didn’t want to do all this. But War had heavy control over her and when she swings down killing Rainbow Dash the ax slices into the stone of Cantorlot.

2000 years past Spike holds the note while he is in a ship with the pods of the Wonder Bolts behind him and he looks at the final words of the letter.

“I am so sorry to everypony that I couldn’t stop the fall of Twilight. I hope someday that many will forgive Twilight even if I can’t. I am sorry…”

Spike drops the letter as he grabs the controls of the ship. Looking outside of the ship watching the battle of Twilights forces and Project Harmony. He takes a deep breath.

“I am coming for you Twilight... “

He quickly flys through the battle to get into the station while many ships fire heavily on the damaged station. The pods slowly start to defrost as Scootloo moves her eyes and she slowly wakes up.

This is the first and last of the Project Harmony stations. It was created to keep peace within our own lives. It failed as we fight for our future. We come and see the future has many stories ahead. The name Project Harmony.

The end continues within Project Harmony.

Introduction: Wake up.

"The world is gone."

The Present.

In the dragon lands on a day of great, great misery. A group of pods seems to be powered by the volcano's lava. A grown-up dragoness known as Ember comes to the tubes and rubs the frost away on one of them, showing ponies in Wonderbolt outfits. It seems the poor creatures went inside these willingly.

A dragon behind her spoke up. "They need us... Princess the queen started her attack on all of Equestria. We need to get them to Harmony one!" She looks to Garbal and nods, softly speaking.

"Get these in the ship that was left here. Fuel it and have Spike fly to Harmony one. We need to protect these heroes of the past. So they can help bring down Twilight and her minions." Garbel nods and flies off to get the ship that Spike can fly. Ember sighs and looks at the six heroes. She's the large ship being carried by Garbal and his friends. It was a big ship that only one can fly... But can hold these tubes. It's a dragon made ship. They have all their ships hidden and it uses lava from Volcanos as it's fuel. He puts the tube from the ship in the lava.

Ember watches as she looks at the Bloodstone ruby. As she grabs an old staff that was part of it along time ago and connects it. She uses it to call the rest of the dragons and has a worried look on her face... She knows when they get to the battle a lot of her kind might be slaughtered since... They never fought the ponies with these advancements.

Spike came in he was still a bit weak but used a crutch to help him along and stared at the tubes.

"Scootaloo?" He blinks and couldn't believe that she was one of the ones in the tubes. "Ember, how long have they been here?"

Ember looks over to Spike and sighs. "Two thousand years."

Spike blinks and Garbel starts pulling them out of the power source. He starts plugging them into the ship’s cargo bay. Scoots open her eyes just a bit to see Spike and try to speak but fall back to sleep.

Spike sighs. "She...vanished before Rainbow's Dash's fate..." Spike gets into the ship and gets ready to fly as he looks to Ember and smiles. "Please stay alive, Ember..."

She nods with a smile and he starts up the ship and flies off into space. When he gets into space all around him there is death. Equestria ships firing on other Equestria ships... He flies right into space to get to Project Harmony. As he flew in space, the cargo in the ship starts to move around and in one of the pods, there is a letter.

"Dear Scootaloo, when you read this, you will learn about my fate... I am sorry that I will never see you again. Maybe it could have been changed? In the past..."