Luna’s protege

by Scootafan

Rating: everyone
Tags: Princess Celestia, Main 6, My Little Pony: Friendship is Magic, Dark, Alternate Universe, Princess Luna, Cutie Mark Crusaders, Scootaloo
Length: 3913

After finding out Scootaloo’s secret, Princess Luna decides to take her under her wing.

After finding out Scootaloo’s secret, Princess Luna decides to take her under her wing. Not content with how Princess Celestial is running the country they decide to plot a rebellion.

Published 2024-01-15 02:20:00 UTC
Last updated 2024-04-08 23:38:41 UTC

Prologue

Princess Luna was walking through the quiet Apple Orchards of Sweet Apple Acres, having had a fun time in Ponyville, celebrating Nightmare Night, she now had a chance to think to herself.

She thought of her sister and scowled, she thought that now that she was back of the moon that Celestia would have changed but no she was still her distant self.

She was angry, Celestial had promised to spend time with her during this Nightmare Night but instead, she had to spend it with her student Twilight Sparkle. Celestial had also promised to change the holiday into one of celebrating the night, not fearing it but that was shot down when she heard that zebra’s legend of Nightmare Moon.

As she was silently ranting to herself, she heard the sound of crying coming from a nearby tree house. Quietly hovering towards the little house, she peered in through the window to find a small, orange pegasus weeping to herself. The filly sniffled “I’m all alone, my parents didn't want me and now my own idol doesn't care about me.”

Luna recognised the filly from several nightmares that she had to rescue her from. She felt sorry for the little Pegasus and felt the same way as she did.

She entered the clubhouse to comfort the sobbing foal. When she entered the filly jumped up in surprise. Turning around, she was shocked to see the princess of the night standing in front of her.

“Hello there, what is your name?” she asked.

“Scootaloo,” she answered, looking away.

“Why are you crying little one,” she asked sympathetically.

Scootaloo wiped her eyes, saying “I’m not crying, big fillies don't cry.”

Luna smiled “There is nothing wrong with having a little cry, I cry all the time.”

“Really,” Scootaloo said incredulously.

“Of course, we wouldn't be pony if we didn't let the sadness out. Now why don't you tell me what the matter is?”

Scootaloo looked around before reluctantly answering “I don't have any parents, they abandoned me when I was young, left me to fend for myself. I always wanted to have Rainbow Dash as my big sister but today she shunned me and told me to stop bothering her otherwise I would ruin her pranks.”

“Scootaloo, a sister who only cares about her pranks than she does, her own family is no sister at all,” Luna told her.

Scootaloo didn't answer, Luna looked around to see a blanket and several old wrappers along with a stuffed toy and a pair of worn saddlebags.

“Have you been living here?” she asked worried for the foal's well-being. Scootaloo nodded looking down at the floor, Luna then exclaimed “I want you to stay with me.”

“What really, at the castle but what would Princess Celestial say?” Scootaloo's asked in disbelief and excitement.

“Yes in the castle and let me worry about my sister,” she replied. She then took the filly in her magic along with all her belongings and teleported straight into her room back at Canterlot Castle.

***

Once they arrived at the castle, Luna placed Scootaloo in bed and tucked her in. Scootaloo’s cheeks went red as she asked “Er, can I have Puddy? I can't sleep without him.”

Luna looked at the stuffed bear and held it up with her magic for Scootaloo to confirm once she nodded she gave the filly the bear who in turn glared at the Princess and exclaimed “Don't tell anypony about this, it will ruin my reputation”

“Don't worry, your secret is safe with me, can't have that reputation be ruined can we.” she grinned.
Scootaloo's nodded knowing full well that Luna was only humouring her.

“Now you go to sleep while I go speak with my sister.”

***

Luna walked into the throne room to find her sister sitting there. “Luna, how did you find Ponyville?” she asked.

“It was well but I have more important matters to address,” Luna told her sister

“And that is?” she asked staring intently at Luna.

“I have brought this pegasus filly home with me,” she explained.

Celestia’s face hardened as she asked coldly “Why?”

“She was homeless.”

“Then take her to an orphanage.”

“Well you see sister, I was hoping to make her into my personal protege.”

“No, you can't take a homeless filly, a Pegasus nonetheless as your protege, it will be a stain on the Royal family.”

This made Luna angry “Of course because if I have anything you have then it's a crime.”

She then stormed out the throne room and went back to her room where she woke the sleeping fully and told her “Cone on, we're leaving.”

“Where are we going?” the filly asked groggily, rubbing the sleep out of her eyes.

“The castle of the two sisters,” she said simply before teleporting them away again.

***

Celestial was seething, angered that Luna had once again disobeyed her. Her thoughts were interrupted by the sound of the doors slamming open.

She looked up to see Twilight and her friends, who didn't look happy at being woken up at this time of night. Twilight yawned, asking “We came as soon as I heard, what seems to be the problem?” she asked sleepily.

“It would appear that my sister is falling back into her own ways and this time she has a hostage.” this instantly snapped the group out of their tiredness.

Twilight stammered “But she seemed so happy earlier on.”

“Exactly too happy, I believe that this holiday has given her motivation to become Nightmare Moon once more.” this made the group gasp.

“Wait a second year Majesty but yer said she had a hostage,” Applejack asked.

“Yes I dont who it is but she told me that it was a Pegasus filly” celestial explained, before ordering them “Get the elements of harmony and find her.”

The group nodded before grabbing the elements, Celestial then told them “I believe she is at the Castle of the two sisters.”

The group nodded before rushing off.

***

In the Castle of the two sisters, Luna had explained everything to Scootaloo, who was stunned, not believing that Celestial could be so cruel.

Luna then asked Scootaloo “Do you know how Celestial has Twilight Sparkle as her number one student?” Scootaloo nodded before Luna asked the ultimate question “Do you want to be my personal student?”

“Yes, but I thought that you needed to be a unicorn.” she said confused.

“While my sister leans towards unicorns, I tend to look at all other races. I will teach you combat and survival skills as well as how to fly, I will also teach you how to channel magic through your wings,” she explained, making Scootaloo more excited, her wings buzzing like a hummingbird.

Suddenly they were interrupted when Twilight and her friends burst in, each of them wearing the elements of harmony.

Twilight exclaimed, “I can't believe you would do something like this.”

Luna told Scootaloo to get behind her as she flared her wings in a protective stance.

Rainbow Dash shouted “Scootaloo! You better not have hurt her.”

Luna merely rolled her eyes before saying “Like you care, you abandoned her”

“Let her go.” Twilight commanded.

“I am not keeping her prisoner, Twilight Sparkle, she wants to be here, isn't that right my number one student,” she said gesturing towards Scootaloo.

Twilight gasped when she said this before asking Scootaloo “Is this true?”

Scootaloo nodded confirming their worst fears, Scootaloo had gone over to the dark side.

“Fine then, if you end up getting banished as well then it's your own fault.” Twilight exclaimed, tears beginning to leak out of her eyes as she was faced with the prospect of banishing a filly. She then finally said, “Come on girls.”

Each of the mane six got into position with Rainbow in stunned disbelief as she faced her number one fan, who in turn glared at her. Twilight started to focus her magic into the elements but was shocked to find that they weren't working. “What's going on Twi, where are the rainbow lasers.” Applejack asked.

“I don't know!” she shouted as she poured all her concentration into the jewellery around their necks but to no avail.

Luna smiled “I guess they don't agree with you.” she said before using her magic to create a force field that basted them out of the castle.

***

Celestia was shocked to see that Twilight had returned in defeat, she was also disturbed at the thought of the elements not working. When she told her about Scootaloo’s act of betrayal, Celestia merely sneered “Then she is a traitor, she will get the same punishment as Nightmare Moon.” causing Twilight to gasp at hearing her mentor speak like this.

Celestial then announced “If the elements aren't working then I am afraid to say that it is war…” making the room go silent.

Chapter 2

Dusk Shade and Princess Luna were both sat in the throne room, strategising on their next move. Dusk Shade told Luna, "Our main problem is not having enough weapons. We should begin attacking equestrian armouries."

"Agreed, however even with your thestrals, we are still greatly outnumbered by the royal guard. We need allies." Luna said.

"How do we find allies, Celestia has too much influence." Dusk was exasperated, annoyed at how little progress they were making.

"Do not be so certain for even Celestia has her own enemies, I'm sure with the right persuasion, we could convince them to join us."

"Who do you have in mind, Princess?" he asked peering over at the alicorn with curiosity etched into his features.

"The changelings would be very useful to have onboard," Luna suggested.

"Are you sure, I've heard that Queen Chrysalis can be a snake."

"That may be true but my sources have already informed me that she has her own spies within Canterlot and the royal guard itself."

Dusk's face darkened, "These sources, wouldn't happen to be that flying rat, would they."

Luna glowered at the thestral before growling, "Might I remind you, that 'flying rat, is my personal protege."

Dusk Shade scoffed kicking dirt in the air, he sneered, "I caught that filly rooting through my personal belongings."

"I assure you that she will be punished accordingly." Luna simply said, not expanding on what punishment she had planned.

"How do you know she is not a spy working for Celestia?" Dusk asked harshly.

"Because I recruited Scootaloo myself besides my sister would never use a filly as a spy." Luna finished with such finality that Dusk knew that the conversation was over. "Now go and consult with your guard about the targets for the weapons." she then ordered and Dusk Shine moved swiftly to carry out his task.

Once he had left, Luna sighed, she knew that she would have to teach Scootaloo that there were consequences for when she crossed the line and that the best way was to make Scootaloo live through the consequences. She was not going to enjoy this, so she then used her horn to send a message to Scootaloo.

She had recently taught Scootaloo how to use her wings to learn different ways of feeling pulses of magic that once made contact with her wings, would then travel up to her brain which would then begin to form words and sentences. Shortly after sending the message, Scootaloo entered the throne room.

"Yes, Princess," Scootaloo said while giving her a deep bow. Luna used her hoof to tell Scootaloo to rise.

Sighing Luna said, "We need to talk about your snooping through Dusk Shade's things."

Scootaloo winced, not long after meeting Dusk Shade, Scootaloo had taken it upon herself to investigate Dusk by searching his personal belongings for any hint of betrayal against their princess, however not only did she fail to find anything usefully, Dusk had caught her red-hoofed looking through his drawers. As soon as he had found her there, he instantly reported her to Luna and had asked her to have her executed for being a spy. Luna however had refused and said that the issue would be dealt with later, something that Scootaloo had not been looking forward to.

Luna then said while giving her a stern look, "Care to explain."

"I don't think he can be trusted," Scootaloo told her, however stopped talking once Luna's face began to contort into fury and her irises flashed electric blue.

"Is this because he is a thestral?" she asked menacingly.

Scootaloo gulped as sweat began to drip down her forehead, "No Princess, I can just feel something off about him."

"So you are telling me that you trespassed into his room and began to search his private belongings because you had a feeling. You should have at least told me before doing something so rash."

Scootaloo stared towards the ground in shame, her ears folded over, she sniffled, "I'm sorry, princess. I won't do it again."

"I know you won't because if you did then you will no longer be my student. Now take it off." Luna commanded.

Scootaloo's eyes widened as she stuttered, "W W What?"

"Take your uniform off."

Scootaloo looked down at her Shadowbolt's uniform before reluctantly taking it off, her uniform was one thing that she cherished as it was the one thing that made her feel like she was family, now the feeling of taking it off made her feel like she was being disowned.

What Luna did next made Scootaloo burst into tears, making Luna's heartbreak as she placed a pair of hoof cuffs onto Scootaloo's hooves along with a pair of magical resistant wing cuffs. She then called for several guards, who arrived and stood at attention.

With a heavy heart, she ordered, "Take her to the dungeons."

She then turned around, not wanting to look at the guards as they began to drag the filly out all the while, trying to block out Scootaloo's pleas for mercy and forgiveness.

Unbeknownst to everypony in the room, a lone thestral was hiding under a window. Upon hearing Scootaloo's cries, Dusk Shade smiled sinisterly, "Finally that brat is out of the way, now all I need to do is take the two princesses out and then I will be the ruler of Equestria mwahaha!"

***

Luna entered the war room, where Dusk Shade told her, "We have found a Royal Guard base that is located on the outskirts of Manehatten, the base contains a large armoury that supplies the forces in the surrounding regions."

"Excellent work, what are their defences like?" Luna asked as she stared down at a hologram of a large military compound that was surrounded by large fences tipped with barbed wire and large guard towers.

"Overall their only defence is the barbed wire fence along with nine guard towers, that are occupied by two guards. There are three guard towers on each fence with four on the front fence that has two of them sitting next to the main gate, which is the only entrance to the compound. 2we are unsure of how many guards, there are but we do know that there are anti-air defences, which include AA cannons and unicorns that are trained at wiping out large swathes of flying creatures at a time.

Upon hearing this Luna began to think of a plan and her eyes lit up as she thought of an idea... She then whispered this plan to Dusk, who instantly scowled upon hearing it. Luna then said, "Tell your thestral's to prepare, we attack in two days."

She then left the room and headed towards the dungeons to deal with Scootaloo...

Chapter 1

After Princess Luna’s revolt, Equestrian was plunged into a mini civil war. Princess Celestia had attempted to attack Luna's fortress head-on, however, the force field proved to be defiant. Meanwhile, Luna had sent Scootaloo into nearby towns and cities, planting propaganda posters as well as attempting to recruit more ponies to the cause. This was proven difficult as Celestia had labelled her as an enemy of the state, not to mention most ponies were still loyal to Celestia. Despite this Scootaloo had found several ponies unhappy with Celestia's rule.

Scootaloo entered the castle, pulling the mask and goggles off her face she exclaimed "It's no use, everypony is still supporting Celestia"

"Don't give up my little pony, anyway I believe I know where I can get an army," Luna reassured Scootaloo, who looked surprised at hearing this.

“Wait you do but I thought that nopony was willing to join.” Scootaloo's said astonished.

“I managed to find a large group of ponies to help us, but enough about that it's time that we continued with your training,” Luna said, taking Scootaloo's into a large courtyard.

She then said “I believe that you are now fully capable of flight and you know how to at least defend yourself. I think it is time that I teach you magic.”

“Really! But I’m only a Pegasus how can I use magic?” she asked uncertainly.

“Everypony can use magic as long as you have something to channel your magic through, for example, unicorns have their horns and pegasi can use their wings,” she explained.

“So can I even do unicorn magic?”

“Yes as long as you have the willpower and the,” mental strength she told the filly. Before the filly could get her hopes up Luna quickly added “However for our first lesson I want to focus on channelling your Pegasus magic as that will be easier.”

“Aww but that's boring” Scootaloo pouted.

“That's only because you have a very different view on Pegasus magic, now enough questions, I need you to concentrate. Close your eyes and breathe in and out.” Luna commanded softly.

Scootaloo nodded and sat down, closing her eyes, she heard Luna whisper, “Flair your wings out and imagine a thunderstorm.”

Scootaloo complied, flaring her wings out making her appear more aggressive, which was helped by the skin-tight Shadowbolt suit, she then imagined herself, sitting in a field with the sound of thunder in her ears.

Luna then instructed, “Now think of the one pony that you hate the most and aim all of your rage towards that pony.”

Scootaloo's nodded imagining both Diamond Tiara, her former class bully along with Rainbow Dash, who she felt had betrayed her. She felt her wings feel static and felt something warm creep through them, she felt her feathers stand on end. Suddenly without warning, she heard a loud crackling sound right in front of her, opening her eyes, she was surprised to see two very large scorch marks on the ground.

Scootaloo sat there in shock as Luna congratulated “Congrats you have officially performed a simple lightning spell, a spell that is commonly used when a pony is on the offensive against an opponent. I must say, I am impressed you managed to perform two at once.”

Scootaloo’s mouth gaped open as it slowly transformed into a smile “I did it, I actually did magic!” Scootaloo's shouted jumping into the air.

Luna couldn't help but smile as she watched the ecstatic filly, unbeknownst to them, a rainbow-maned pegasus, wearing a Wonderbolt suit was sat watching the duo, just outside of the force field. She frowned before zooming off, leaving a rainbow trail in her wake, which went unnoticed.

***

Celestial was sat in the war room staring down at a hologram of the Everfree Forest as she strategised on how to bring the force field down.

Rainbow Dash joined her, still wearing her wonderbolt attire, she told the princess “You're gonna wanna hear this princess”

Celestial got up and followed Rainbow to the briefing room where the rest of the mane six was waiting for her. Once they were all seated Rainbow Dash announced “Scootaloo can do magic.”

This led to gasps of disbelief as Twilight blurted out “But that's impossible, she’s only a pegasus”

“Trust me Twilight I saw it with my own eyes, she caused several lightning bolts to appear by themselves, similar to the ones that Nightmare Moon used against the guards during the summer sun celebration,” she explained.

“Well, then she has to have had a cloud.” Twilight stammered trying to use her overused brain to figure it out.

“She didn't, there wasn't a cloud in sight”

Twilight gripped the side of her head as she repeated “But that's impossible.”

Celestial sighed before speaking up “My sister must have taught her how to use magic with her wings.”

Everypony looked at her confused at what she just said with Applejack exclaimed “Ah’m sorry, come again?”

Celestial explained “Pegasi can channel magic through their wings similar to how unicorns use their horns”

Rainbow asked, “If pegasi can do that then why haven't we been using it against her?”

“Because it is incredibly dangerous, so dangerous in fact that I outlawed it”

Twilight didn't know what to believe, her mentor seemed so cold and distant.

***

Princess Luna and Scootaloo both arrived in Hollow Shades under the cover of darkness, Luna was disguising herself through her cloak, whereas Scootaloo was wearing her full Shadowbolt suit, her golden goggles, enchanted to see in the dark.

They walked into the local town hall to find a dark grey, thestral with a deep purple mane. “Scootaloo's this is Dusk Shade, he is the mayor of Hollow Shades and he comes from a long line of fellow supporters. He has promised me to provide us an army using his own citizens.” Luna explained, she couldn't read Scootaloo’s expressions because of the suit but she felt that she was confused.

Scootaloo's asked “Is he a vampony?”

Dusk answered for Luna “No, I am a thestral, while we look similar to vampony we do not drink the blood of ponies although we aren't against eating meat.”

Scootaloo made a disgusted face, hidden by the mask but Luna reassured “The thestrals are often misunderstood and interpreted as monsters but I assure you that they are no more dangerous than you or me”

She then further explained, “Thestrals keep to themselves, preferring the darkness of the White Tail Woods, Thestrals are also very loyal to the night which in turn means that they are very loyal to me.”

Dusk added “Celestia, kept us shunned away and promoted the rumours that we feed on pony flesh, forcing us to stay in hiding. That is why we want our revenge and are willing to help Princess Luna in every way possible.” He stomped his hoof on the floor making the room shake.

Scootaloo sensed that the thestral wanted more than revenge “What's the catch?”

“There is no Catch all I want is for the thestrals to be able to live and roam freely from discrimination and fear.” He explained, however, Scootaloo wasn't all too convinced, however, she decided to give him the benefit of the doubt.

***

Princess Celestial was outraged, she had found out that Hollow Shades along with the thestral population had risen up against her and publicly announced their support for Princess Luna. “I should have slaughtered them all when I had the chance! It doesn't matter now, they will be dealt with soon, I just need to bring that force field down along with my sister and that stupid filly. Once that force field is down, Luna will be begging to be sent to the moon as for the filly, well accidents happen and accidents can be tragic…”