Mystery Over the Unicorns

by Catpaw616

Rating: teen
Tags: Thriller, Original Character, Mystery, Spike, Starlight Glimmer, Adventure, Violence, Princess Celestia, Twilight Sparkle, My Little Pony: Friendship is Magic, Alternate Universe
Length: 4945

As the days go by, unicorns have been reported missing across Equestria. Insistent to save her friends and the other innocent unicorns, Twilight, along with Spike, set out to find the cause. However, they soon won't be alone on their journey.

Unicorns have gone missing all across Equestria, and no one seems to know why.

After a talk with Princess Celestia, Twilight and Spike set out to find the cause of the disappearances. However, as the search continues, they encounter a potential companion...

Will Twilight and Spike's mission succeed? Or will they fail and be one of the victims?

Special thanks to Forcalor for coming up with the title!

Published 2023-04-27 07:30:00 UTC
Last updated 2023-08-23 20:41:50 UTC

Prologue

It was a gloomy night in the Everfree Forest. The winds calmly blew through the trees, and the animals were all quiet in their nests. Except for the owl, who hooted to no one in the cold night.

However, the owl wasn't the only one awake in the forest. Deep inside the Everfree Forest was a skinny orange unicorn carrying a unconscious pony on it's back. It finally set the body on the ground when two other ponies showed up. One was a slightly bigger orange-red unicorn, and the other was a azure-colored unicorn, who stared down at the body in disappointment.

"You were supposed to tie their hooves so they don't run away!" He angrily told the orange unicorn, who backed away in fear.

"S-Sorry, Azul. This is my first time doing this—" The orange pony stammered, then he was interrupted by a scoff from a orange-red unicorn.

"I knew that it was a risky move: sending him to kidnap a pony. We've gotten so far into this plan. It's only a matter of time before some inexperienced newbie ruins it." he scowled while he stared at the frightened unicorn.

"You better thank the stars that he was unconscious still. If he ran off, we would've been screwed for sure." Azul muttered as he grabbed the rope and wrapped it around their hooves, and carried him to a giant, wooden cart.

"We have to be more careful than usual. This is the part of Equestria that gets really dicey." Azul told the two.

"How is it different than the rest of the places we visited? asked the orange-red unicorn, who was named Thistle.

"Ponyville is one of the most populated towns in Equestria. It is the home of the ponies who wielded the Elements of Harmony. The Princess of Friendship even has a castle there!"

"Who cares? We'll rob Ponyville as easily as the other places." Thistle scoffed once more. Then the orange unicorn boldly stepped in.

"Um, hello? That place is home to Rarity, the Element of Generosity, and Twilight Sparkle! Those are two very important unicorns that we have to capture!"

Thistle bared his teeth in a snarl, which frightened the unicorn more. "In case you somehow forgot, Twilight is an alicorn, and we have made a rule to not go after them yet."

"But won't Twilight notice the missing citizens and eventually find out about us?" the orange unicorn asked, but it made Thistle even angrier for some reason.

Azul nodded in understanding as he faced Thistle. "You have to admit, Apricot does have a point. Which is why we won't steal as many—"

The orange unicorn looked stunned by what he said. "My name isn't Apricot! It's Riverdale—"

"Too bad. We've decided to call you Apricot because it seemed more fitting than... whatever you said." Thistle told him while chuckling to himself.

"Back to the point..." Azul rolled his eyes in annoyance. He turned to Apricot. "You are correct, concerning about Twilight's nosiness. But Ponyville is necessary. Ponyville has Rarity, and we can't leave without Rarity."

"What about the rest of her friends? It's not just Twilight we should be concerned about." Apricot asked.

"Relax. Without Rarity, they can't use the Elements onto us. Therefore, we are stronger if we fight them individually. Especially the weak one." Thistle told him.

"Even so, we will find a way to deal with them." Azul told the two of them. He shook his head while he smiled. "Twilight may be an alicorn, but I don't think she'll be matched against the three of us."

"You mean the two of us. I doubt Apricot would hold up." Thistle joked. Apricot rolled his eyes.

Azul looked doubtful. He cleared his throat and with his magic, he levitated a map from the cart. "Anyways, after we raid Ponyville, I decided that I want to make a special trip."

Thistle tilted his head. "I thought we were going to Canterlot afterwards."

"We are, but then a town popped into my mind and I just couldn't resist." Azul told him. He opened up the map with his aura, and when he showed it to his companions, he put his hoof on a little village with two rows, and with one house in front of the rest.

""There. That's where we're going next,"" He told them.

Apricot looked confused, meanwhile Thistle started laughing.

"Seriously? That's the special trip? That's the most blandest town I have ever seen!" He laughed while he playfully punched Apricot's shoulder.

Azul rolled his eyes once more. "Yeah, laugh all you want. But this town is home to a certain particular unicorn."

Apricot's eyes suddenly widened in interest. Even Thistle stopped laughing and looked serious.

"Go on." he said.

Thankful that he's finally starting to listen, he began his story. "Before I met the two of you, I was a traveler. I ventured the cold mountains, looking for a place to stay. Until finally, I saw a quaint, tiny town. Just like this one." he explained while he tapped his hoof onto the town.

"Then once I arrived, I was met with... weird smiles. All of them were staring at me in a creepy manner, and all of them had weird haircuts. But what shocked me the most is that all of them had their cutie marks as equal signs."

"But before I could even look around the village, or even ask what was going on, I met a mare. She was a unicorn—"

"You had me at unicorn!" Apricot raised his voice. He later got bonked in the head by Thistle, shushing him.

"Yes... anyways, she was a unicorn. From the moment I saw her, I knew that something was not right. Her coat and mane were brighter and vibrant than the rest, and even though she was welcoming, she always gave off a negative vibe... but despite that, I wanted to stay for one night because it was the only local town nearby."

"So, she wanted to tell me something. She encouraged me to follow her into a cave for a 'talk.' I followed her and before I could even react, she used this random stick and used its magic onto me. I was stunned and I couldn't move. Then I felt my cutie mark being ripped off of my own body! It hurt a lot and I felt my energy drain away in a flash."

"But... that's impossible! A cutie mark can't be taken away like that!" Apricot protested.

"I didn't want to believe it either, but it happened. But don't worry, while the mare was foolishly boasting about her success, I had enough willpower to fight back with my hooves. I caught her off-guard and I tackled her to the ground. Thankfully, she dropped the stick and my cutie mark popped right back. Before I could give her the chance to retaliate, I ran away from the cave, swearing revenge for trying to make me 'convert' in her town."

"So if this mare has the stick, then she could take away our cutie marks..." Thistle pondered. He looked at Azul in a fierce expression. "She could potentially ruin our plans."

Azul nodded grimly.

Apricot got up and rushed over to Azul. "Things will be ok, Azul. Think about it. As we know, this mare is living way over there," he said while he pointed at the town. He then dragged his hoof to the area that said "Everfree Forest"

"And we're all the way over here! Besides, I think that unicorn isn't that strong enough to take on the three of us."

"For once, I agree." Thistle agreed as he walked over to the two. He looked ahead to see a view of a distant Ponyville.

Azul looked at his companions. "So is it settled?"

Both of them nodded.

Azul nodded back. "Very well."

All of them looked at Ponyville from the distance. They watched silently as the wind blew through their manes. Then one by one, they disappeared into the darkness.

Chapter 1

1 week later...

Ponyville News!

Not even a day had passed and there's already a case of missing ponies all across Ponyville!

The victims include Lyra Heartstrings, Twinkleshine, Minuette, Sea Swirl, and Amethyst Star!

"We all have to be on guard as we walk on the streets of Ponyville. We don't know whether all of these ponies left willingly, or some other pony or creature has captured them. Either way, we should be aware of our surroundings for the time being, and if you see any suspicious activity, please report to me or the princesses at once. -Mayor Mare.

Why are these ponies going missing? Who is responsible? And what will the princesses do about this alarming manner?

Twilight grumbled as she tossed the newspaper away and hopped out of the bench seat. This is the third time this week that there had been reports of ponies going missing. First it was Apple Stars and Cherry Spices, and yesterday it was Silver Spanner, Neon Lights, and Ocean Breeze; now another band of ponies have went missing a day after. She had hoped that Celestia and Luna would deal with this matter right away, but so far, they've done nothing to make the crime rate go down.

Spike, who had just finished eating a sapphire cupcake, got out of his seat and followed the distressed alicorn.

"Gee, Twilight? What's wrong?" Spike asked as he caught up to her.

Twilight sighed. "It's these reports about the missing ponies. More and more keep disappearing every day. So far, Celestia and Luna have done nothing about it."

"Maybe they're trying to figure out who the culprit is." Spike responded as he shrugged his shoulders.

Twilight shook her head. "It's been a week since this started. If anything, the culprit should've been found right now."

Spike now looked confused. "Why are you so dependent on them? Shouldn't you find out about the culprit yourself? I mean, you are a princess after all."

"Of course, I offered to help find the culprit, but Celestia told me that 'due to me feeling fatigued about stopping another villain', she decided to let me take the time off and let her do something for once." Twilight responded with an eye-roll. "My journey to the village and back wasn't even that bad!"

"Oh." Spike responded with a low voice. He remembered the story of how Twilight and her friends arrived at a village that had ponies with the same cutie mark. Then a unicorn named Starlight Glimmer took away their cutie marks, and forced them to live in a solitary home until they "converted" to her philosophy. "But I'm sure the culprit isn't even that powerful, or scary. Just random ponynappers." He told her. Then he patted her arm as she continued walking. "Besides, you have your friends! If you could take on Chrysalis, Tirek, and Starlight, then I have doubt that they will be an exception."

Twilight sighed once more, but she looked grateful at the dragon. "Thanks Spike." She said as a reply. I just hope Celestia has this in the bag.

As an attempt to clear her mind, she decided to take a stroll in the park. She and Spike looked around, smiling as the warm, spring sun bathed the area. Although Twilight's mood dampened when she saw Bon-Bon sit next to another earth pony by the name of Junebug. Bon-Bon was crying on a bench, while Junebug tried to comfort her.

"This is where me and Lyra used to sit. We sat weirder than most ponies, but we didn't care. This was our favorite spot in the park." Bon-Bon said as she tried to fight back the tears.

"Don't worry, Bon-Bon. Lyra will be back eventually." Junebug tried to calm her down, but it didn't seem to work. She turned to Twilight and gave her a grim expression, not sure what to do.

Spike looked around the area. He saw a few ponies who also mourned their missing friends and family, but it was not a new sight for him. It had been happening all week. "Yeah... the culprit needs to be stopped sometime soon. I don't want to see depressed ponies everytime I go to the park."

"It's not just here, Spike. It's everywhere." Twilight told him. She could practically hear the wails outside her walls whenever she tried to go to sleep at night.

"Oh, tell me about it, darling." a new, familiar voice spoke up. The two saw Rarity trot up to them in a worried manner. "This has been going on for days. How long before Celestia stops the crime?"

"Hopefully soon." Twilight told her as she sat down onto the cold wet grass and the others followed suit. "How is your business going, Rarity?" Twilight asked, trying to change the subject.

Rarity shrugged. "Eh. It's not very active recently. Everyone is spending less time on buying clothes and more worried about the disappearances that have been going on across Equestria."

Twilight's eyes widened. "Across Equestria? What do you mean?"

Rarity looked alarmed. "You haven't heard?"

"About what?" Spike asked curiously.

Rarity took out a crumped-up newspaper from her purse and showed them an article that said:

Manehatten Times!
Ponies continue to go missing by the day!

Rarity turned over the page and started reading. "According to this article, it says that 'ponies have been disappearing from time to time in Manehatten. Police are launching investigations about the crime. As of now, police have found that the missing victims from each disappearance turn out to be unicorns. Coincidence, or a connection?'"

"Hold on a tick." Spike raised his hand to stop. He turned to Twilight. "Who went missing yesterday?"

Twilight tilted her head, confused by his behavior. "Lyra Heartstrings, Twinkleshine, Sea Siwl, Minuette, and Amythest Star?"

"And what about the rest of the victims here in Ponyville?" Spike now asked Rarity.

Rarity too looked baffled by his behavior. "Um... Silver Spanner, Apple Stars—"

"And are they unicorns?"

"Well, of course they—" Rarity stopped midsentence as she realized the point Spike was trying to make. "Yes... all of them are unicorns."

Spike immediately sprang up. "I can't believe it!" he turned to face a confused Twilight. "Twilight! I think we found our first clue! They're only after the unicorns!"

Twilight raised her hoof to silence the dragon. "Now, hold on. This seems like a stretch. Surely they must've captured an earth pony, or a pegasus."

Rarity shook her head as she continued to read the newspaper. "I think Spike might be on to something. The missing victims in Manehatten are unicorns, and so are the victims in Ponyville!"

"Sure there can be no connection to this..." Twilight muttered in disbelief.

"Twilight, you said that you wanted to help out with the cause. Now this is your chance! You can tell Princess Celestia about this new clue!" Spike encouraged her.

"But what if they go after the other races next? I'm pretty sure they're not only after the unicorns." Twilight argued. "Besides, I'm sure Princess Celestia knows already."

"It can't hurt to try, darling." Rarity replied.

Twilight looked at Spike, then back at Rarity. Both of them looked intently at her. Reluctantly making up her mind, Twilight sighed in defeat and rose from the ground. "Fine, we'll go tell Princess Celestia. But don't say I didn't warn you when she chides at us for wasting her time on facts she knows about."

Author's Note

Please comment down below if you found any spelling errors and grammar mistakes. It would help a lot!

Hope you enjoy the story so far! Positive and constructive criticism is always accepted! So don't be afraid to be harsh. I do want to get better at writing after all ;)

Chapter 2

Of course I know it's only the unicorns! I'm not stupid!

That was probably what Twilight was expecting to hear once they told Celestial about this "new" clue. She heavily despised disobeying her former mentor by putting her nose in places where she doesn't belong. Unfortunately for her, her friends were persistent to tell.

But who knows? Maybe this is a clue that Celestia didn't know, and if Twilight and her friends can notice details that Celestia didn't... then maybe...

No. She told me to rest, and that's exactly what I'm going to do. Twilight firmly told herself. Then she looked around the Canterlot castle... and she kept thinking about the newspapers that Rarity brought with them. But it's easier said than done.

Rarity, who noticed Twilight looking down, wrapped a hoof around her neck in a sympathetic manner. "Don't worry, Twilight. Even if she dismisses the clue, at least you're trying to help the cause, even if you can't go."

But Twilight didn't feel moved by her words. "I think that's the problem..."

As they neared the throne room, Spike's head perked up, suddenly alert. He ran ahead and reached the closed doors. After listening what was inside, Spike looked at the two ponies with a worried expression.

Confused, Twilight and Rarity eavesdropped by putting their ears on the cold, metal door. They heard shouting and outcries from the room. Twilight fought the urge to slam the doors open and demand what was going on, but what was stopping her was the audible protests she can hear.

"Unicorns are disappearing all across Equestria and so far, you're doing nothing!" a male pony spoke in outrage. Twilight quickly recognized the voice of Fancy Pants, and he's most likely talking to Celestia about the same problem.

But she definitely knows about our "new" clue. Twilight thought. Normally she would immediately leave without any hesitation, but something inside told her she should stay... and so she did. Hopefully I won't get in trouble.

"Why don't you send Twilight and her friends? They are perfectly capable of stopping crime than you could ever be in a thousand moons!" Twilight heard a female pony speak in an outraged manner.

"For all we know, these ponynappers may capture children next!" Twilight recognized the worried voice of Mayor Mare.

"Everyone, please! I know the situation is bad, but—" Celestia tried it explaining, but she was interrupted by another cry of outrage.

"We know the situation is bad! Everyone in Equestria knows, and it's about time you do something about it!" The same female voice argued.

"Yeah! It's been happening for at least a month, yet so far these crimes haven't stopped!" Mayor Mare agreed.

Rarity backed away from the doors and walked to the direction of the exit. "Maybe we should come back a little later. She seems to be busy at the moment..."

But Twilight remained still. She looked back at Rarity in a determined expression. "I need to step in."

Before Rarity and Spike could stop her, Twilight slammed the doors open with her magic. Once she did, all of the ponies inside looked at her in confusion. Especially Princess Celestia. Twilight suddenly felt regret rise in her body.

"Twilight! What are you doing here?" The ruler asked in a confused manner.

Despite the regret she's now feeling, she managed to walk over to Celestia with her head high. She tried to ignore the three pairs of eyes that were staring at her from behind.

"I wanted to talk to you." She told Celestia. She tried her best to not make her voice squeak from fear.

"And so do we." Spike added as he and Rarity rushed inside, as they arrived, they stood by Twilight's side, as if in a way to protect the purple alicorn for Celestia's upcoming anger.

"Finally! Someone is about to do something with this matter!" Fancy Pants spoke approvingly, with Mayor Mare, and the female pony nodding in apporval.

Ignoring them, Celestia looked down to face Twilight. "What are you doing here? I'm a little busy at the moment." she said.

"We can tell. But we also want to share our concerns about the crimes too." Rarity replied. She quickly wrapped her hoof around Twilight's neck, much to the latter's shock. "We want to help!" Rarity exclaimed.

Celestia looked stunned by her request. The Princess turned to see the three outraged ponies stare at her in unamusement.

"Leave it to the Elements of Harmony to deal with the crimes for Princess Celestia." The female pony rolled her eyes.

"Couldn't agree more, Florence." Fancy Pants agreed. Mayor Mare, on the other hand, looked sympathetic.

Celestia looked down at Rarity in disapproval. "This is not the best time."

Rarity looked dismayed. "When is the best time to offer help?"

"When I'm not busy with protestors." Celestia answered. Celestia turned her head to face a guard, who was at her side the entire time. "Can you escort these ponies outside for a moment? I want to discuss with these three alone."

The guard nodded. He got out of his position and went up to the spectating ponies.

"Where are you taking us?" Florence asked in disapproval.

"Outside. Celestia will discuss with you three in a moment." The guard responded briskly.

Once the they were out the door, Celestia looked down at Twilight in disapproval. "I thought I said that I can deal with the matter myself. You need to rest after you've been through the trouble with that village."

Starting to feel annoyed, Twilight couldn't fight the urge to facehoof. "Celestia, Starlight wasn't even close to the likes of Chrysalis and Tirek. Those two were harder to beat yet I was fine and ready the next day."

"But it makes me feel like you're doing all the work for me when I'm supposed to be the protector of Equestria." Celestia argued. Her eyes were now widened with worry. "Even if you are a Princess who can do just fine on your own, I'm always worried whenever you try to stop these villains. I should've been the one to stop Starlight this time."

"But they were called by the Map!" Spike decided to step in. "The Map decided to send the six of them. Not you."

"But I could've stopped her from escaping." Celestia pointed out. "Now she could be hiding in 'me knows where'. Or so that's how you say it."

"But she's just a unicorn. She doesn't seem like a mythical creature." Twilight argued.

"Can we talk about Starlight and the village later? That's not the reason we're here." Rarity told the two in a firm voice.

After the awkward silence, Celestia sighed as she rose from her throne. "Twilight, I get that you and your friends want to help. I really do. But not only do you need a break from fighting crime, but ponies are starting to question my authority as a protector now. If I want their trust back, I have to fix this crime myself. You doing the job for me will only make things worse."

Twilight could only stand by in utter silence, and so did Rarity and Spike. The three looked confused at one another. She never acted like this before...

"Celestia, I know a way to really help—" Twilight tried to reason with her, but she was only met with slammed doors.

Author's Note

Please let me know if you spot any spelling and grammar errors!

Positive comments and constructive criticism are appreciated as always!

Chapter 3

"I can't believe that happened," Twilight muttered as she rested her head on the mushroom table. Twelve pairs of eyes stared at the disappointed alicorn in shame.

After Celestia had dismissed them, she brought her friends to the café and ranted about her worries to them. If Celestia wasn't going to listen, at least her friends were around as a backup plan.

"So, you think someone is kidnapping these unicorns?" Fluttershy asked in a terrified manner as she covered her eyes with her wings. Twilight had no idea why she was so deathly scared about it. As far as she knew, she wasn't a planned target due to her kind.

"But why?" Applejack tilted her head. The orange earth pony gave Twilight a concerned look as she ruffled through her hat that lay on her head. "And who would steal 'em?"

"Whoever it is, I would like to come face-to-face with them right now!" Rainbow Dash shouted as she flapped her wings. Twilight flinched at how hard she slammed the table. "I'd like to see them try to take Rarity!"

Rarity's eyes widened when she heard that. She looked around nervously as if expecting these kidnappers to appear at any moment.

"We should add security cameras around Ponyville. Maybe they'll catch the ponynapper!" Pinkie Pie said cheerfully, despite the fearful mood that hung over the group.

"That could take hours, if not days to do." Spike objected with a sigh. "And it would cost a lot of bits." He said, laying his chin on his hand.

"So, what now? We just can't sit here and do nothing." Rarity asked the group, still looking terrified. "If Celestia can't help us, we might as well do it alone."

"That's the problem, Celestia doesn't want us to help," Twilight told them in an irritated manner. "She believes that we've solved enough of her problems so much that her people are starting to lose their respect."

"Well, yeah. She's supposed to be the protector of Equestria." Applejack responded. "Dealing with criminals is her job."

"So, she wants us to do nothing?" Rainbow Dash slammed the table with her front hooves in outrage once again.

Twilight and Spike shrugged helplessly.

Applejack sighed, taking a sip of her drink. "She'd better stop these thieves before another missing case occurs. Rarity might be next." She noted, eyeing her friend.

"She's not going anywhere as long as I'm around!" Rainbow Dash boasted as she firmly wrapped her hoof around Rarity's neck.

The unicorn now looked very uncomfortable.

"You can't protect her forever," Fluttershy muttered to Rainbow Dash, which took Twilight by surprise.

"Aren't you a ray of sunshine?" Rainbow Dash huffed as she recoiled her hoof and sat back in her seat.

"So, what's the plan?" Rarity asked, seemingly eager to change the subject.

Twilight shrugged again. Normally she would be creating a detailed plan right about now. As much as she wanted to, she knew that this was not the right time.

"I know this may seem bad but... I don't know. Maybe Celestia should handle this on her own." Twilight hesitantly began. When her friends opened their mouths to object, she silenced them by raising her hoof. "I've thought it through, and Celestia is right. We have been taking care of her problems lately, and I think that we should keep out of it."

Her friends were silent this time.

Twilight slammed her face onto the mushroom table again. She was now torn between letting Celestia handle it or doing it herself.

Her friends said nothing throughout the whole dinner, although they were giving each other unconvinced looks.

Twilight and Spike were heading back home. Twilight's head hung low as she walked. Spike took pity on her and began to rub his claw onto her shoulder.

"Cheer up, Twi." Spike tried reassuring her. "I'm sure things will work out in the end. They always do."

"It's not just that, Spike." Twilight stopped walking and looked pitifully at her friend. "I have no idea what to do. If I let Celestia handle it, my friends will object. If I insisted and worked out the problem ourselves, Celestia would object. I'm betraying one of them depending on what I do."

"Twilight, you're not betraying anyone." Spike tried to reassure her, but it didn't seem to work. Twilight continued to walk back to the castle with the same dejected momentum.

Spike shook his head helplessly. He didn't know what to say next that would help, so he followed the alicorn silently into the castle.

However, he saw a dark shape move from the corner of his eye. Spike quickly turned his head to see the shape, but it disappeared as quickly as it reappeared.

That was when he heard low, indistinct voices from the shrubs not too far away.

Without a moment to lose, Spike ran up to catch up to Twilight and gently yanked her tail. "Uh, Twilight?" he said nervously.

Twilight stopped and looked down at the dragon. "What is it?"

"I hear voices," Spike said urgently. "Over there." he pointed at the bushes.

Twilight slowly approached the bush, her ears perked as she listened carefully for these voices. However, she couldn't hear anything but the wind and an owl hooting in the distance.

"I don't hear anything, Spike." Twilight gave him a perplexed look.

"Whoever's making the voices most likely went silent when we were around." Spike marched up to the bushes and dug his claws into the leaves. In a flash, he poked his head into the shrubs.

He found nothing.

Twilight looked a little amused by the scene.

Spike now was very bewildered. "I... I swear I thought I heard something!" he stuttered.

"You most likely imagined it." Twilight came up to him and gently pulled Spike away. "Come on, it's getting late."

At first, Spike didn't want to move away, but he reluctantly followed Twilight back to the castle anyway. He occasionally glanced back suspiciously at the bushes, eager to know what he just heard.

I've sworn I've heard voices. Male, hushed voices. Spike pondered in his mind, still staring at the shrubs, which were now far away.

Author's Note

Shorter chapter than usual, but I wanted to make build up for the next chapter, which will hopefully be longer.