The Enigma

by Fox0427

Rating: everyone
Tags: Adventure, Derpy Hooves, Crossover, Doctor Whooves, Main 6, My Little Pony: Friendship is Magic, Dark, Other, Original Character
Length: 3806

Fox Shine's co-worker/boss betrays him and blackmails him into creating a formula for a dangerous experiment. The fate of Equestria is now in the hands of three ponies...

Fox Shine is called in to his work and needs to spend a week on a secret project for his co-worker/boss who ends up blackmailing him. He is forced to give his boss a dangerous formula which is used conduct an experiment that puts the entirety of Equestria in danger... Now, only three ponies can save it. Doctor Whooves, Derpy, and Buttercup hold the fate of Equestria in their hands.

Published 2013-07-27 20:00:02 UTC
Last updated 2013-08-13 22:15:12 UTC

Prologue

Prologue:

Two ponies stood glaring at each other in an underground laboratory. Their manes are identical, and their cutie marks similar. The pony on the right is a pegasus with dark orange skin, brown eyes, a dark brown mane, and his cutie mark is an open book, representing his creativity. The one on the left is a unicorn with dark green skin, red eyes, a dark blue mane, and a piece of paper on a clipboard filled with scientific information his cutie mark, representing his love for science.
"Give it to me. NOW." The unicorn speaks with anger in his voice.
"No!" The pegasus speaks sternly, and almost drops a scientific formula he's hold in his mouth. "It's too dangerous to let fall into the wrong hands! I won't give it to a mad pony like you!"
"Well, you're not going to use it, so why did you make it? We both know the answer..." He smirked. "You made it... For me. I told you to make it, and you did. You work for me. Now if you could hand it over, please."
"NO! I won't! In fact, I'm quitting, and taking this home with me to destroy! Nopony should ever have this, and I should've quit the second you told me to make this! I DON'T KNOW WHY I EVER DECIDED TO WORK WITH YOU IN THE FIRST PLACE, SO BETTER LUCK NEXT TIME!" The pegasus turned and headed for the stairs to the surface, but was stopped in his tracks when he heard the unicorn laughing.
"Haha! Oh, Fox Shine! Here I thought you had learned all of my tricks, but I guess not!" The unicorn burst into laughter again. It took him a while to calm down before he could more seriously say, "I knew you wouldn't give it to me. It was obvious."
"And?" Fox Shine talked angrily, but he was more confused then angry. "So? What are YOU going to do? If you set up some sort of trap to capture me and take it from me, then I can try to avoid it now. So if that's what you did, then you're a fool."
"A trap? No, no! Nothing like that! It's more of, well, it COMPLETELY is, blackmail."
The unicorn began to laugh again, but as he laughed, his laugh began to sound creepy, and demented.
"Blackmail? N-no! You don't-... You wouldn't-" Fox Shine turned around. He was suddenly more angry than ever. "Don't hurt her."
"Oh, I won't hurt your precious daughter. Unless you don't give that to me." He stepped toward Fox Shine. "She's in the holding cell. Oh, yes, and her fillysitter is in there too. You should have chosen a fillysitter who wasn't so easy to tie up. I mean, seriously. She thinks I can be stopped if she STARES at me."
"HOLDING CELL?! Since when did this place have a HOLDING CELL?!"
"Oh, it's always had one. I made sure it was hidden from you though. If you found out, you could've seen this coming."
"W-wait... You mean... You planned this since the beginning?"
"Of course I did! I do that with everypony I work with!"
"You mean you've done this to other ponies? But... Why?"
"I've already told you too much! I can't tell you my master plan! I shouldn't even have just told you that I have one!"
"Something tells me you'll be making sure I don't tell the royal guard, too."
"Of course. A pony did that once. They aren't a pony anymore."
"Wait, W-WHAT?! You- but- I- HUH?"
"I turned him into a Timberwolf. That way, there was no way he could talk, everypony would run from him, and there was no body of any sort, so nopony really knew what happened to him. Genius, is it not?"
"You... You're not mad... You're more than that... You're-"
"Enough chitchat! Give me the formula, and tell nopony. Your daughter and friend already no not to tell anypony as well, so I'll let them go as soon as you give that to me."
"But... How do I know I can trust you to let them out?"
"I told you enough chitchat. Put it down, and wait outside."
Sighing, Fox Shine dropped the formula and walked up to the surface. He better let them go, or he'll pay! Fox Shine sat at the top of the stairs and waited for them to come up the stairs. I'll give him five minutes.

A Short Chat

Chapter 1: A Short Chat

"Of course, Fox Shine! That won't be a problem." Fluttershy knew she had trouble once when Applebloom, Scootaloo, and Sweetie Belle was here, but she was sure she could take care of Buttercup. It was only one filly this time. "Thanks, Fluttershy. I hope she doesn't give you trouble!" Fox Shine turned to leave, and Fluttershy felt Buttercup's purple mane brush on her as Buttercup walked into the cottage.
"Wait, why will you be gone for a week?" Fluttershy hadn't thought of that before. She knew she better ask now, because she sure wasn't going to get a chance when he was gone.
"Oh, I was told by my boss that he wanted me to complete an important task, and that I'd probably have to stay at the lab so I don't forget about the task. I don't know what it is yet, but my boss sounded like he REALLY wanted it completed."
"Oh, alright. Wait, where do you work anyway? I don't know much about you. I only know who you are due to Pinkie Pie, and the party she threw to welcome you to Ponyville."
"Yeah, I didn't understand that party. I moved to Ponyville before she did. Anyway, I work in a laboratory in the Everfree Forest"
"Th-the Everfree Forest?! Be careful on your way!"
"Don't worry I will be!" Fox Shine walked off towards the Everfree Forest and called out, "Tell Buttercup I'll see her in a week!"
"I will!" Fluttershy called back, before shutting the door. Fluttershy turned to Buttercup and smiled. "So, Buttercup, what do you want to do?"
"I wanna fly!" Buttercup excitedly exclaimed.
"You want to... Fly?"
"Yeah! Fly! I wanna be the best flier in Equestria! Can we fly over the Everfree Forest? It'd be really fun!"
"No! That's much too dangerous!" I should change the subject. Fluttershy thought. "Oh, by the way, your dad said he'd be back in a week."
"What? Too dangerous? What's dangerous about it? It ain't like we're goin' into the forest! Besides, notin' is too for Buttercup!"
"We're not going into the forest." That didn't work. "I'm sorry. I'm telling you, it's too dangerous." Fluttershy thought for a moment. "Hey, wait, don't you have a mom that could watch over you? Is she busy too?"
Buttercup rolled her eyes. "I'm adopted."
"Oh. Uh, okay. So... You want to fly?"
"Yeah! I wanna fly! I wanna fly 'til I'm as good as ma role model!"
"Oh? Who's that? Your dad?"
"Nah, he never flies. It's kinda stupid, ya know?"
"Um... So, who's your role model?"
"Ma role model is none other then Rainbow Dash! Ma dad brought me to see the Best Young Fliers Competition, and that Sonic Rainboom was phenomenal! Just wait, and one day, Buttercup will be the best flier in Equestria! She'll be able to do a Sonic Rainboom in ten seconds flat! No, faster than that!"
"Um... Your third person is starting to remind me of Trixie..."
"Trixie? Sorry, dunno who that is, but I can stop if ya want."
"Oh no, it's fine. Just ignore that."
"Ya know, if all we're gonna do is talk, shouldn't we sit on your couch or sometin'?"
"Oh, I guess so. Have you eaten yet?"
"Nah, and I am pretty hungry. Maybe I should eat before we fly. We are flyin', right?"
"Sure. Let's get you something to eat first, though."

"Are you sure?" Fluttershy asked. She wasn't certain it was a great idea to fly through the mountains. It wasn't as dangerous as the Everfree Forest, but still.
"Yeah! Ma dad brings me here all the time!"
"I thought you said he didn't fly much, though?"
"He doesn't. He watches me fly around. Again, kinda stupid."
"So, there isn't anything... Dangerous? Like dragons? Quarray eels?"
"Nah, quarray eels live in Ghastly Gorge. And dragons? I never seen one 'round here, so nope. Although, I'm sure it's possible for one of those creatures to live 'ere. Wouldn't that be awesome? I've always wanted to see a dragon! Seriously, they're almost as cool as Rainbow Dash!"
"D-dragons aren't awesome at all! Th-they're really, REALLY sc-scary!"
"Oh come on, they ain't scary! Oh, whatever, let's just fly already!"
"But, we already are flying!"
"We're flyin' in place! We ain't movin'! It ain't fun like this! I wanna feel the wind in my mane, and do barrel rolls! Now that I think of it... I wanna find a dragon! Come on!"
"W-what? No, wait-" Fluttershy watched as Buttercup dashed away and began searching the mountains. "Wait up!" Fluttershy quickly flew after Buttercup.

An Idea Dawns

Chapter 2: An Idea Dawns

Fluttershy got out of her bed and sighed. This filly really likes to fly. I'm not used to flying so much, and so fast! Fluttershy went downstairs and sat on the couch. I guess she isn't up yet. Hopefully we can do something different today. I hope she enjoys tea parties... Angel jumped up onto the couch and demanded to be pet. Fluttershy stroked him, and thought while she did. She came up with an idea, and thought she would definitely try it when Buttercup woke up.

Yawning, Buttercup walked down the stairs, to find Fluttershy waiting for her. "Um... Why are you sittin' there lookin' at me?"
"I've been waiting for you to get up so we could do something again!"
"Oh... Um... Okay. What are we gonna do?"
"Well, that's up to you! We could have a tea party, we could play Shhhh, we could fly again, or-"
Buttercup rolled her eyes. You even need to ask that question? "Let's fly! Well, I'm really the only one flyin' your just sorta... I dunno, not goin' very fast."
"Are you sure? I have one more idea!"
"Yes, I'm sure!" I don't care what your other idea is! Let's just fly! Buttercup thought.
"But I'm sure you'll love it!"
Buttercup sighed. Fine, if it'll make ya happy ya crazy pony. "Alright, what is it?"
"Well, I'm pretty much best friends with Rainbow Dash, and we could-"
"WHAT?! Why didn't ya tell me this yesterday! Can we go look for her? Wait, does she live here in Ponyville? I thought she lived in Cloudsdale! Was I wrong about where my own role model lives? Ohmygoshohmygoshohmygoshohmygosh! Come on! Where is she?"
"Well, um... Yeah, she lives in Ponyville. Well, her house is on the outskirts of Ponyville, but she spends most of her time in Ponyville. We can go look for her."
"OHMYGOSHYESTHANKYOUFLUTTERSHYYOU'REAMAZING!"
"Um... I think you should calm down a little."
"Oh... Um. Sorry. Yeah I'll stop freaking out. But still, thanks Fluttershy! You truly are amazing!"
"Wait, did you-... Never mind."

Fluttershy lead Buttercup through Ponyville, while keeping an eye out for Rainbow Dash. She noticed Twilight walking towards her library, and stopped her.
"Hey Twilight." Twilight probably knows where Rainbow Dash is.
"Hey Fluttershy. Who's the filly?"
"Fluttershy, I thought we were lookin' for Rainbow Dash."
"This is Buttercup, she's the daughter of Fox Shine. I'm fillysitting for him."
"Fox Shine? I don't know who he his, but ok."
"Fluttershy, are you ignorin' me?"
"Oh, I'm sorry. We are looking for Rainbow Dash, I'm going to see if Twilight knows where she is."
"Oh... Alright."
"So um... Twilight, do you know where Rainbow Dash is?"
"Sorry, I don't. In fact, I didn't see her at all yesterday, and I haven't seen her yet today."
"Aww..." Buttercup moaned. "Let's keep looking Fluttershy."
"Alright. Thanks anyway Twilight."
"Good luck finding her! She'll turn up sooner or later."
Buttercup looked up at Fluttershy and said, "If nopony has seen Rainbow Dash since two days ago, doesn't that mean she could be in trouble? Maybe she's sick."
"Just because me and Twilight haven't seen her for two days, doesn't mean nopony has seen her for two days. We can still ask Pinkie Pie, Applejack, and Rarity."
"What about other ponies?"
"Well, actually, I'm not sure how many other ponies really know Rainbow Dash very well."
"Oh, okay... Hey... Wait." Buttercup and Fluttershy stopped walking for a second. "Do you hear that?"
Fluttershy listened intently and heard a humming sort of sound fading in and out, before coming to a stop. "It was probably nothing. Let's keep going."
"But, I've never heard anything like that." Buttercup turned around. "Hey... Was that there a second ago?"
Fluttershy also turned to see what Buttercup was looking at, and saw a strange blue box that said "Police Box" on the top of it.

Doctor Whooves

Chapter 3: Doctor Whooves

The Doctor opened the TARDIS door and jumped out. "Here we are Derpy, back in Ponyville."
"Yeah, we've come back here after every adventure, so it was pretty obvious we were coming here." Derpy walked out and stood next to The Doctor.
Suddenly, a purple maned filly ran up. "Hey, where did you guys come from? That box wasn't there a second ago, was it?"
Another pony ran up and said, "Buttercup, it was probably just our imaginations. There's no such thing as a teleporting box. Let's go look for Rainbow Dash."
The filly sighed. "Can we at least look inside the box?"
The Doctor quickly closed and locked the door, then said, "Oh, it's nothing interesting, just... A box."
"But... You were both in there, wouldn't it have been crowded?"
"Um... Buttercup... I think we should just go..."
"Uh, yes! It was... very crowded inside the TAR- the... the box." Derpy replied.
"The... Tar? It doesn't look like tar."
The Doctor exchanged a glance with Derpy. "Um, we have to go." The Doctor ran around a nearby corner into an alley, and Derpy followed close behind. "You almost told her about the TARDIS!"
Derpy lowered her head. "Sorry."
The Doctor sighed. "It's fine. I shouldn't have had the TARDIS teleport in plain sight during this time of day. We're lucky they're the only ones who noticed."
"So... What do we do now?" Derpy asked.
Um... I don't know." The Doctor thought for a moment. "Doesn't something bad usually happen soon after we get back?"
"Yeah, usually. Nothing bad has happened yet. Maybe we should go on another adventure?"
"We can't just jump to conclusions! We only just got back!"
"But when we just got back is usually when something bad happens! Remember? Nightmare Moon, Discord, That time we visited Canterlot and there were Changelings, it was all right after we got back from an adventure on another planet!"
"Usually doesn't mean always!"
"Well, yeah... I guess you're right. Actually, no. You ARE right."
"Yes. I'm also The Doctor."
There was silence for a while, until The Doctor said, "So, what shall we do while we-"
"HEEEEEEEEEELP!"
The Doctor's eyes brightened. "That's our cue!" The Doctor ran back out the alley, tracing the scream, and leaving Derpy behind.
"Doctor, wait up!" Derpy dashed out the alley as well, and looked around, but was unable to spot The Doctor anywhere. "Doctor? Doctor! Where'd you go?"
"HEEEELP ME!" At the sound of the second scream, Derpy caught something out of the corner of her eye. She turned to see what it was, and asked, "H-hello? Is someone there?"

"HEEEELP ME!"
The Doctor turned one final corner before bumping right into another pony.
"Ah! Get out of the way! It's right behind me!" He blurted out.
"What is? There's nothing behind you!"
"Wha- what..." He turned to look behind him. "W-where... Where did it go? It disappeared!"
"Ok... You need to calm down, and tell me what happened."
"Uh... O-ok... I was walking near the Everfree Forest, because it's part of my daily walking routine path, and a creature jumped out of the forest and started chasing me!"
"What did it look like?"
"Well, it had randomly appeared out of nowhere, and it kind of scared me, but even more so after it began to chase me!"
"Ok, but what did it LOOK like?"
"It had a spider-like body, and its head was a huge tentacle! That's um... All I remember."
"Well, I've never heard of a monster like that... What do you think, Derpy?" The Doctor looked around. "Derpy?"

Sanity is not Pink

Chapter 5: Sanity is not Pink

"Pinkie Pie should be here, and if we're lucky, maybe Rainbow Dash! We come here pretty often, actually." Fluttershy explained as they walked up to Sugar Cube Corner.
"I still feel like something bad may have happened to Rainbow Dash. That'll seem even more true if none of your other friends have seen her in a while either!" If something has happened to Rainbow Dash, it would be amazing if I saved her! Being in her debt would be cool! But... Maybe Fluttershy is right, what are the chances Rainbow Dash is in trouble... Buttercup thought.
"Buttercup, nothing has happened to Rainbow Dash."
"Why don't we just go to her house?"
"She spends most of her time in Ponyville, it's quite unlikely she'd be at her house."
"Hm."
They walked into SCC, and Buttercup immediately noticed a messy-haired overly-happy pink pony standing behind the counter.
"Hey Pinkie."
"Hey! Who's the little filly?" The pony continued to smile, and it began to creep Buttercup out. I've never seen somepony so happy... It's like one of those horror shows where there's a pony who's so happy, but there's something extremely odd about them. Also they usually go insane and kill ponies.
"This is Buttercup. I'm fillysitting her."
"Oh! Fox Shine's adopted daughter! Oh, of course! It says that in Chapter 1! Silly me!" Pinkie burst out laughing.
Buttercup cocked her head. There's the odd part. "Umm... What?"
"Don't you remember? It said: Chapter 1: A Short Chat and Fluttershy was talking with Fox Shine, then he left to go to his work, and then Fluttershy was talking to you!"
"...Your talking as if this a book or something." Ok, so she's even odder than the ponies in the horror show. She must hold a world record for Most Nonsensical Pony Ever.
"Oh, this isn't a book! It's a Fanfic!"
Even Fluttershy looked confused. "A... Fanfic?"
"Oh, never mind! Anyway, let me think for a second... Oh! Chapter 2, you thought of the idea to introduce her to Rainbow Dash! But you can't find her, because later in Chapter 8... Oh! Well then... Chapter 5... I'm supposed to say... Oh! Ok..." Pinkie changed her expression. "Rainbow Dash? I haven't seen her in over three days!"
Buttercup noticed Fluttershy seemed to pretend like everything before that was never said. I'll... Just do the same. Buttercup thought.
Fluttershy pondered the statement for a while, before saying. "That's odd... Nopony seems to have seen Rainbow Dash in quite a while."
"See what I've been sayin' Fluttershy? She could be in some sort of trouble!"
Hey, wait... Pinkie said something about "later" in Chapter 8, something about Rainbow Dash. She also said this was Chapter 5, so maybe she can tell us what happened! Wait, no... She's insane! And now I'm thinking like a mad pony too!
"Hey! I'm not insane!" Blurted Pinkie.
"But you-... Wait... How did you...?"
"Hey Fluttershy! Maybe the filly is right!"
Fluttershy gave Pinkie a confused look. "You mean... Maybe you really are insane? I didn't hear her say that, but-"
"No, not THAT! Maybe Rainbow Dash IS in trouble! We need to look for her!"
Well, maybe she DOES have some sense in her.

You Again?

Chapter 4: You Again?

"HEEEEEEEEEELP!"
Buttercup froze. "What was that?" She looked up at Fluttershy.
"I-I don't know! We should get out of here!"
"Get out of here? No way! Someone might be in trouble! We gotta go help 'em!"

"But it's dangerous!"
"Exactly!"
"W-what?"
Buttercup turned around and tried to think where it had sounded the cry for help had come from, but couldn't remember.
"HEEEELP ME!"
"Ah! There we go!" Buttercup got it now, and ran towards it.
"No! Buttercup! Wait!"
Ignoring Fluttershy, Buttercup ran through the streets of Ponyville, and managed to confuse her self every now and then, but eventually, she turned a corner and stopped.
"Hey, it's you again! Your that pony that came outta that blue box... It was called The Tar, right?"
"Umm... Yes! But, what are you doing here, little filly? You should go, it's dangerous! I'm The Doctor by the way! Hey, wait, didn't you have another pony with you before?"
"The... Doctor? Doctor... Who?"
"Just The Doctor!"
"The Doctor? That's it?"
"Well, some ponies call me Doctor Whooves, actually, but I prefer The Doctor, or just Doctor."
"...What..."
"Umm... Doctor?" Buttercup jumped when she heard another pony talk. She hadn't even realized there was somepony standing behind The Doctor!
"Oh! Right! Again, you should leave, filly, it's dangerous right now, and I'm awfully busy!"
"How is it dangerous? I heard someone cry for help, but I can't see why, and I'm pretty sure this is where-"
"Buttercup!" Buttercup recognized Fluttershy's voice, and thought she must be looking for her.
"I'm over here, Fluttershy!" Buttercup turned around, and after a few seconds Fluttershy came around the corner.
"Buttercup! Please don't run off like that again! I was awfully worried!"
"Oh come on, Fluttershy! You could've followed me easily, right? I mean, you should be faster than a filly like me, shouldn't you? Don't tell me your slow at flying AND running!"
"Buttercup, you shouldn't have run off to somewhere that could possibly be dangerous! You could have been hurt if there was some sort of monster!"
Buttercup sighed. "Sorry, Fluttershy. But, I LOVE running into danger! My dad actually considered changin' ma middle name to danger! Danger is fun!"
"Well, don't please try not to."
"Alright, I promise I won't."
Fluttershy stepped past Buttercup. "I'm sorry, sir. I hope Buttercup didn't get in your way."
"Oh, it's fine."
Fluttershy turned and began to walk away. "Come on, Buttercup. Let's go look for Rainbow Dash again."
"Alright. Hey wait, if somepony was in trouble, what that pony was being chased by a monster? What if that monster had got Rainbow Dash! That would explain why she went missing!"
"Buttercup, the only place near here with monsters is the Everfree Forest, and they never seem to come out unless lured out. I doubt Rainbow Dash went into the Everfree Forest."