The Master Plan

by SparkBrony

Rating: everyone
Tags: Adventure
Length: 4365

Three of the baddest villians in Equestria team up to take down the Mane Six once and for all.

In this epic tale, three old enemies long banished from Equestria return, seeking revenge on those who wronged them, especially the Mane Six, who they plan to eliminate once and for all.

Published 1970-01-01 00:00:00 UTC
Last updated 2013-04-07 13:57:16 UTC

Chapter 1 - The Letter

"Yeeha!"

Apple Jack ran through the west field of Sweet Apple Acres, the wind whipping through her mane, tossing seeds left and right, while Big Mac pulled the plow along behind her. The sun was shining, and the temperature was just right. The soft soil was kicked up by Apple Jack's back legs as she ran so freely through the field. She skidded to a perfect stop as the pair reached the outer edge of the field.

"Beautiful day, ain't it Big Mac?" Apple Jack asked as she stared happily at the morning sun shining off the sides of the bright red barn in the distance.

"Eeyup," answered Big Mac, brushing the dirt from the field off his hooves. He then proceeded to detach the plow from himself.

Apple Jack was excited. Planting season had rolled around again, one of her most favorite times of the year, next to harvest. Every year, she never failed to love planting across the whole farm with her brother. The two made an unstoppable and effecient team. One day, Apple Jack mused, maybe her little sis would be running alongside them too.

A familiar yell brought the orange farm pony out of her reverie. "Aaaaaapple Jaaaaaack!" Granny Smith called from the distance. "Time fer lunch!!!!!"

"C'mon Big Mac," Apple Jack said to her brother, grabbing the empty seed packets and adjusting her hat. "Time to head on inside and wash up."

"Eeyup," the large red stallion said again. They ran across toward the farmhouse.

~  ~  ~  ~  ~

After cleaning themselves off from their work outside, Apple Jack and Big Mac joined the others gathered around the table to eat. Granny Smith had whipped up yet another delicious apple-related entre.

"So, how's things with the Cutie Mark Crusadin'?" Apple Fritter asked Apple Bloom as Granny Smith handed out plates piled with food.

"Ain't bad," replied Apple Bloom, picking at her food. "We tried soccer cutie marks today, but....nuthin'."

"Shucks," said Apple Fritter. "Well, I know y'all will get your cutie marks soon, don't worry."

"I know, I just wonder how long it'll take," sighed Apple Bloom. She turned to her food and began to chow down.

"Aw, look, the ol' MailPony's here!" cried Granny Smith, looking out the window.

"I'll get it!" said Apple Jack, jumping up from her seat. She ran outside and intercepted the Mailpony as he rifled through his bag for their mail.

"Thank ya kindly," she said as the Mailpony pulled out several letters and packages and handed them to her.

"Sure," said the Mailpony. "Oh, one more thing. This letter addressed to you is labeled 'URGENT'." He handed her a small envelope.

"Thanks," said Apple Jack, waving goodbye as he walked away. She took another look at the letter and noticed it was addressed to her and Apple Bloom, and it was from Babs, her sister's favorite cousin!

"Apple Bloom!" She said as she walked back in. "Ya got a letter from your cuz, Babs!"

Apple Bloom's eyes nearly popped out of her head. "My cousin Babs!" She cried happily. She snatched the letter out of Apple Jack's hooves and tore open the envelope. Anxiously, she began to read. Apple Jack watched her eyes move from side to side as she skimmed the lines of the letter. As she got further and further down the page her eyes got wider and wider. By the time she finished there were tears brimmming in her eyes.

She looked up at her sister. "Apple Jack!" she cried. "Babs is in big trouble!!!"

"What?" said Apple Jack in suprise. "What do ya mean, in trouble?" She grabbed the letter back and quickly skimmed through it. It read:

Dear Apple Bloom and Apple Jack,

This is very urgent. Somethin' wierd's goin' on here in Manehattan, and I need you guys to come as quickly as you can. Please, I really need your help!

Your Cousin,

Babs Seed

Apple Jack looked up from the letter. Apple Fritter and Big Mac stared at her. Granny Smith was too busy knitting to notice anything that was happening.

"What do we do?" cried Apple Bloom, tears running freely down her cheeks now.

"There's only one thing to do," Apple Jack replied, setting the letter on the table and putting on her hat. "Get to Manehattan as fast as we can".

"We're gonna see Babs?!" squealed Apple Bloom, quickly changing from her saddened state.

"We sure are," said Apple Jack. "Get your stuff together, we're leavin' as soon as possible.

"For Manehattan? Just like that?" asked a bewildered Apple Fritter.

"Babs is lil' sis's favorite cousin," said Apple Jack as Apple Bloom zipped around the room, gathering what she'd need for a suprise trip to Manehattan. "If she needs help, we gotta be there to help her as soon as we can. Even if it means goin' a long way on short notice."

Apple Fritter smiled. "Well, y'all have a great time there! we'll be waitin' here for y'all when ya get back."

"Eeyup," agreed Big Mac.

(Granny Smith had noticed none of the conversation, she was still too absorbed in her knitting.)

"Thanks y'all," said Apple Jack as she and Apple Bloom headed toward the door. "We'll be back before ya know it."

They waved goodbye and the two sisters headed for the train station to catch a ride to Manehattan.

Chapter 2 - The Picnic of Panic

Meanwhile, Twilight Sparkle was having problems of her own.

"Where'd I leave that book?" she cried frantically as she rushed back and forth across her library.

"Calm down," Spike encouraged. "I'm sure it's around here somewhere."

"I cannot calm down!!!! I have to memorize that book in three days!!! How am I going to - Oh, there it is." Twilight picked it up off her desk where it had been all along.

Spike burst out laughing. "It was there ALL ALONG!!! How could you have missed it?" He rolled around on the floor, clutching his sides.

Twilight glared at him an turned back to her desk. Suddenly, Spike burped up a letter, nearly frying Owlicious with hot green fire in the process.

"Hey!" he exclaimed. "It's from Princess Celestia!"

Twilight picked the letter up off the ground and began to read it aloud:

Dear Twilight Sparkle,

I just wanted to write a quick letter to you about some recent events in Equestria you may not have heard about. Lately, there have been several disappearances of ponies in both Canterlot and Cloudsdale. They usually disappear during the night and we fear there may be ponynappers on our hooves. I don't mean to frighten you, I just wanted to warn you to take extra precautions in Ponyville both night and day. My royal guard will hopefully be able to sort this out.

Sincerely,

Princess Celestia

"Wierd," commented Spike. "Ponynappers? That's, like, the most ridiculous thing I've ever heard."

"It's quite unsettling," said Twilight. "I should probably tell the others about this. Oh, hey, Pinkie's picnic is today! I can tell them then!"

"When is it?" asked Spike.

"It's at....." Twilight trailed off as she examined her clock. "Now!  Aagh! Quick, Spike, we're gonna be late!" She and Spike hurried out the door, heading for the park.

~  ~  ~  ~  ~

"Hey! Look everypony! Twilight's here!" cried Pinkie Pie happily as Twilight Sparkle and Spike arrived at the picnic, exhausted from practically sprinting all the way there.

"Sorry I'm late, girls," Twilight huffed breathlessly, plopping down on the picnic blanket between Rarity and Fluttershy.

"No problem! Except Rainbow Dash ate all the muffins already," Pinkie said.

"I don't really mind," replied Twilight. "Anyway, I got an important letter from Princess Celestia today." She pulled it out of her bag.

"Uh, it's ok Twilight, this picnic is supposed to be fun, not a boring storytime," said Rainbow Dash as Twilight unfolded the letter.

"This one's really important, just listen," Twilight told her. Rainbow rolled her eyes. Just as Twilight was about to start reading, Rarity let out a scream that startled her so much she dropped the letter.

"What is it? Is everything ok?" Twilight asked.

"NO! It's NOT ok! Look!" Rarity held out part of the sundress she was wearing for them to examine.

"Um, what's wrong with your dress?" Fluttershy asked the question that was on all of their minds.

"What do you mean? Can't you see that horrible grass stain?!" Rarity cried.

"You mean that teensy meensy eensy weensy green spot?" Pinkie asked.

"TEENSY?" Rarity was outraged. "It's simply ENOURMOUS!" Of all the horrible things that could happen this is THE. WORST. POSSIBLE. THING!"

Rainbow facehoofed. "Quit being such a drama queen, Rarity!"

"Um, guys? Important letter from the Princess, remember?" Twilight reminded them as Rainbow and Rarity began to argue loudly.

"Hey, where's Apple Jack?" Spike changed the subject yet again from Twilight's letter.

"Oh, she had some last minute plans!" Pinkie yelled over the sound of Rainbow and Rarity's debate.

"GIRLS!" Twlight shouted. Immediately, everypony was silent.

"Finally," she breathed. She smacked the letter down on the picnic blanket and began to read. When she finished, she looked up at their concerned faces (Well, all except Pinkie, who was gobbling down a sugar cookie.)

Everypony was silent for another minute, taking it all in. Then -

"Ponynappings?! In Cloudsdale?!" Rainbow exploded. "This is insane!" she jumped to her hooves angrily.

"It is serious," agreed Twilight.

Pinkie suddenly stopped happily chewing her sugar cookie. "Serious?" she said, almost as if seriousness was an alien thing to her.

"What should we do?" asked Fluttershy. "I don't want the ponynappers to come to Ponyville and harm my critters!"

"I'll tell you what I'm gonna do!" declared Rainbow Dash before anypony could say anything. "I'm going to Cloudsdale to help out! No pony messes with us pegasi!"

Maybe Rainbow has a good point, thought Twilight. Maybe I should do the same. Her brother, her sister-in-law, and all the friends she had had growing up were there, after all.

"I think I should go to Canterlot too," she told the others. "You know - since Shining Armor's there, I want to make sure he's all right and everything.

"We'll stay here and PARTYYYYYY!!!" exclaimed Pinkie. "Um, I mean, protect Ponyville!"

"I'd rather not tussle with any so-called ponynappers," said Rarity, "But I simply must take care of Sweetie Belle."

"So it's settled," Rainbow declared. "Twilight will go to Canterlot, I'll go to Cloudsdale, and the rest of you will stay here.

Sounds good to me!" She spread her wings, and with a flash of a spectrum of colors, took off into the bright blue midday sky.

"Well, she's anxious," Twilight observed as Rainbow became no more than a speck in the distance.

"She is the element of Loyalty, after all," Rarity said. "She'd obviously want to protect her hometown."

"True," said Twilight.  "Anyhow, Spike - gather my things. We're catching the first train to Canterlot."

Chapter 3 - Rainbow Crash

Rainbow Dash zipped through the sky. She shoved clouds out of her way as she flew past them. I have to get to Cloudsdale as soon as possible, she thought. They're in danger - they need me! What if her friends had been taken? Lightning Dust, Snowflake, Derpy? She desperately hoped not. They had to be safe, they just had to!

"Whoa!" Rainbow swerved around a large incoming cloud. Previously the cloud had been blocking her view of the sky ahead of her. Now she saw that a volley of dark, menacing storm clouds were between her and Cloudsdale.

Great, thought Rainbow Dash. Just great. Well, there's nothing else I can do. I'll just go through the storm. She began to pick up speed. I've done like a hundred times before anyway! She reassured herself.

By this time the black clouds were quite close and Rainbow could hear the thunder from them and see the sheets of rain that were pouring down. Wierd... she thought. I thought I controlled the weather in this region too, and I didn't plan for any rain!

But she had no time to reminisce on the subject, as right then she shot through the outer layer of the storm clouds.

Haha, this is the life! she thought as the rain poured over her and adrenaline coursed through her body. Whatcha gonna do, storm? I'm not afraid of you!

Then she got hit by lightning.

The shockwave from it threw her off course and sent her sailing through the black clouds. Hey, no fair! She tried to righten herself but felt a sharp pain in her wings as she did. Slowly it began to fade. But not before she got hit again. And again.

Ow! That really hurts! she grunted in pain. The lightning seemed to be tracking her, striking her again and again no matter what she did! And the thunder sounded vaguely like....laughter?

She dodged another stream of unrelenting voltage, but like a heat-seeking missile, it found her and struck her again! Right then, she knew she couldn't take any more. The pain was too great. Her wings stopped flapping abruptly and she dropped out of the sky. But she never hit the ground. The storm clouds swallowed her just as she began to lose conscienceness. Seconds before she went under, she heard it.

Laughter. There was no mistaking it.

~  ~  ~  ~  ~

Twilight Sparkle's train slowed to a smooth stop at the Canterlot station. She turned to Spike, who was loaded with her bags.

"Finally! We're here Spike! Ready to see the Princess?" She asked.

"No," Spike replied indignantly. "I was taking a nap, for crying out loud!"

Twilight chuckled. "Well, too bad. Seriously, you get enough sleep at home, while your napping on the job!"

The two stepped out of the train. Canterlot station was very elegant. Groups of sophisticated-looking ponies walked by them as they walked toward Canterlot Castle, not far from their stop.

"Wow! Canterlot never fails to look beautiful on any occasion!" Twilight observed as she stared in awe at the looming castle.

"Yeah, yeah, whatever," Spike replied. Twilight shook her head, unphased by him. Then she noticed several figures at the castle gates.

"Oh my goodness!" She gushed. "It's Princess Luna and Princess Celestia!" She began to run down the path. "Wait up!" cried Spike. "I'm the one carrying all these suitcases!" He did his best to lug Twilight's gear after her.

"Twilight Sparkle!" Princess Celestia exclaimed in suprise as Twilight came into view. "What are you doing here?"

"Indeed, I could ask the same!" added Princess Luna. "Shouldn't you be at Ponyville?"

"Princess Celestia sent me a letter about the ponynappings in Canterlot and Cloudsdale, and I came as fast as I could!" Twilight explained as a breathless Spike caught up to her. "Is everypony ok?"

"We were just about to come to Ponyville," said Princess Celestia. "Something terrible has happened."

"Oh no!" Twilight's fears were confirmed. "What?"

Princess Luna put a hoof on Twilight's shoulder. "It's Shining Armor," she said. "They took him."

Chapter 4 - Bad Seed

At about the same time that Twlight Sparkle was arriving in Canterlot, Apple Jack and Apple Bloom's train was just beginning to slow into the Manehattan station.

"I can't wait to see Babs!" Apple Bloom exclaimed. She peered out the window eagerly, looking through the bustling crowd outside for her cousin. She reminded Apple Jack slightly of a small, yellow Pinkie Pie.

"I just hope she's okay," Apple Jack added.

They exited the train along with a dense group of babbling city ponies. They spilled out into the busy train platform. The farm sisters gazed up at the unbelievably tall skyscrapers around the station.

"This place is amazin'!" Apple Bloom cried. "Those buildin's are so big!"

They were both looking up at them in awe when they heard a familiar heavily-accented city pony's voice. "Apple Bloom!"

Babs Seed barreled through the crowd of ponies and tackled Apple Bloom in an exited hug. The two fillies then scrambled to their hooves and bounced happily up and down.

"Alright, alright," said Apple Jack. "Babs, ya sounded like ya were in a pickle when we got your letter. What's wrong?"

Babs turned to the older sister. "I gotta show ya," she replied. "Here - come to my apartment and I'll tell you everything."

"Ok," agreed Apple Jack as a sophisticated-looking business pony pushed past her. "I wouldn't mind gettin' outta this crowd anyway.

They walked across the platform and exited the station. They emerged into a busy sidewalk clumped with ponies of all kinds.

"Seems like every place in Manehattan is bustlin' today!" noted Apple Jack. Babs nodded in agreement. She was only half-listening as she was also carrying on a conversation with Apple Bloom. The younger farm sister chattered about school and the latest activities of the Cutie Mark Crusaders. Oddly, Babs looked bored with her tale. Apple Jack thought this was a bit strange; she expected both fillies to be babbling away. But she quickly dimissed this skepticism, as she knew Babs was probably a little worried about her problem - whatever it was.

"Well, here it is! My apartment building!" announced Babs when they arrived in front of one of those famous Manehattan skyscrapers.

"It's huuuuuuge!" Apple Bloom's eyes were wider than a healthy apple at harvest season.

"I know," said Babs. "But luckily I live on the first floor. I hate stairs."

Apple Bloom seemed a little crestfallen that they wouldn't be able to go to the top floor of the building, but nothing could phase her out of her happy, excited aura. They walked into the building and Babs walked them to the door of her apartment. She inserted a key, turned the knob, and entered the room.

Babs' apartment wasn't anything too special. There was a large living room, stairs at the back up to the bedrooms, and a kitchen off through a doorway to the left.

"Just look out that window and you'll understand my problem," said Babs, gesturing toward a window on the other side of the room. The view out of the window was obscured by curtains.

"Ok," said Apple Jack. She and her sister started across the room.

Halfway there, the floor caved in.

Apple Jack let out a yelp, suspended in midair, before she and Apple Bloom hit the concrete floor - hard. Both let out grunts of pain as the landing took it's toll. Apple Jack's head was spinning, but she managed to lift hereslf to her hooves and look around. They seemed to be in a basment of some kind, but it looked more like a dungeon. She gazed up and about six feet above her was a hole in the ceiling, where she could see Babs' apartment and Babs' face peering down at them.

"We're ok!" Apple Jack assured her. "What happened? How are you?" Apple Bloom began to stir beside her sister on the basement floor.

"Oh, I'm better than ever,' Babs replied, grinning down at them. Her eyes narrowed and she smiled sinisterly? Or was Apple Jack seeing things?

"Babs....?" Apple Jack repeated. "Are you...."

"Oh, you can stop calling me that now," Babs called down to them.

"What's going on?" said Apple Bloom, sitting upright now.

"Oh, Apple Bloom," Babs sighed. "Well, I said I'd tell you everything, didn't I? Hmm, I have a better idea. Let me SHOW YOU!"

At 'show you' Babs' voice turned into one Apple Jack recognized. Not a good one. And then things got wierd.

Green light shot from Babs' eyes and mouth. A sinister green mist surrounded her. They watched as she got bigger, her mane got longer, and holes appeared in her legs. Fangs erupted from her mouth and her eyes turned torquoise. A jagged horn emerged from her forehead. Her transformation was complete.

They had been tricked.

Queen Chrysalis laughed down at them. Apple Jack and Apple Bloom stared, horrified, up at what they thought had been their friend.

"Thanks for playing, but I'm afraid it's game over!" She said in her double voice. The apartment floor folded up like a trapdoor above them and left them in darkness.

Except they weren't alone.

Chapter 5 - She's Our Friend Too

Twilight Sparkle paced anxiously back and forth across the Canterlot throne room. Princess Celestia and Princess Luna looked on worriedly as the purple mare muttered to herself.

"This can't be happening! He can't be gone! What am I going to do?" Twilight panicked.

"Please, dear, it'll be alright," Celestia assured her. "We already have multiple highly-trianed search parties looking for Prince Shining Armor right now. Her words didn't seem to settle Twilight down though.

"I know how you feel, honey," said Princess Cadence, who had entered the room not long before. She now sat next to a worried Luna. "I'm as worried about Shining Armor as you are. But I know Celestia's guards will find him."

"I just don't want him to get hurt!" cried Twilight. "It's not like before, when Chrysalis cursed him; he was still there with us. Now we don't know what hos captors are doing to him!" She collapsed in a teary, sobbing mess.

"Shining Armor is very strong and resiliant," Luna said. "He can protect himself. I am sure he is fine."

"Who do you think ponynapped him, anyway?" asked Princess Cadance.

"I have a feeling it's no new group," said Celestia. "I think it's some villian we've fought before." Her words sent a chill down everypony's spine.

Just then, the giant double doors to the throne room flew open, and a messenger stallion rushed in.

"You have news?" Celestia asked him.

"Yes, Princess. We have searched the castle and the entire villiage, as well as the outskirts of Canterlot, but we have not found any of the missing ponies," the mesenger reported.

Celestia sighed. "None of them?"

"None, Princess," the guard said solemly. "Is there another place you would have us check?"

"Where else is there?" Celestia seemed to almost have given up hope when suddenly Twilight jumped to her hooves. Everypony in the room stared at her.

"Did you check the Crystal Caves?" she asked.

"Sorry? The....what?" The messenger guard seemed puzzled.

"You know, the caves under Canterlot! The ones that Chrysalis trapped Cadance and I in when she was getting married!" It seemed like a pretty good place to hide someone to Twilight.

"I doubt the Captain even knows they exist!" the guard exclaimed. "I'll tell him immediately!"

"Wait! Cadance and I will come with you! We know the caves better than anypony else," Twilight said as Cadance stepped to her side in agreement.

"It's very dangerous. I don't think you should go," said the messenger.

Cadance and Twilight looked at each other for a second, then back at the guard. "I think we can handle it," Twilight replied.

"If you say so," The guard answered. "Come on, we don't have much time."

"Good luck girls," Celestia called after them as the two ponies nodded at her and followed the guard out the door.

~    ~    ~    ~   ~

"Apple Bloom's really late! I wonder where she could be!" Sweetie Belle exclaimed.

"It's not like we can start the meeting without her...." Scootaloo frowned.

The two were waiting in the clubhouse for the commence of their next important meeting. The only problem was, their leader was not present.

"Maybe we should go to Sweet Apple Acres," suggested Scootaloo.

"I don't know," Sweetie Belle replied. "What if she's doing some important family stuff?"

"Or..." Scootaloo jumped to her hooves, eyes wide.

"Or what?" asked Sweetie Belle.

"Or what if she broke her legs bucking apple trees, and she's lost in the apple orchard, and the Apple family is trying to find her, but they can't and they need help!" Scootaloo clapped her hooves to her head.

"That's pretty far-fetched," Sweetie Belle began, but before she could say anything more, Scootaloo swept her onto the back of her scooter and zipped out of the Clubhouse and down the street.

"Whooooaaa! Woooohooo!" Sweetie Belle cried as the wind whipped past her. Scootaloo swerved around annoyed ponies and ducked under large mares like she was riding through an obstacle course. The buildings and houses of Ponyville rushed past them in a blur. Every once in a while, ponies ahead of them jumped sideways to get out of the scooter's path.

Scootaloo stopped suddenly as they zoomed past a certain pink pony. Sweetie Belle looked over at Pinkie, who was staring intently at a mailbox without blinking.

"Umm, Pinkie? What are you doing?" Scootaloo asked.

"I'm making sure this mailbox doesn't attack Ponyville!" Pinkie told them as if it was the most obvious thing in the world.

Scootaloo raised an eyebrow and looked at Sweetie Belle. "Okay....I think we better....be going now....Seeya Pinkie."

"M'kay, have a great day!" Pinkie told them, her eyes never leaving the mailbox.

Scootaloo and Sweetie Belle hopped back on the scooter and zipped away. It wasn't long before they dodged their way to Sweet Apple Acres.

The two filles parked the scooter and popped off their helmets. Then they rushed up to the farmhouse and knocked anxiously on the door. Seconds later, it was opened by a smiling Apple Fritter.

"Howdy girls, what's goin' on?" she asked the fillies.

"We're looking for Apple Bloom. Is she okay?" asked Scootaloo.

"She was late for our meeting," Sweetie Belle chimed in.

"I'm sure she's right as rain, but she's not here," Apple Fritter said. "She went to Manehattan with Apple Jack."

"MANEHATTAN?" cried the fillies.

"Yup. Got a letter from Babs sayin' she was in trouble or somethin'," Apple Fritter replied.

"BABS?" cried the fillies again. Apple Fritter chuckled.

"We have to go help her!" said Sweetie Belle.

"Yeah! Babs is our friend too!" Scootaloo added determinately.

"I'm sure you'd love to go, but what about your sister, Sweetie Belle? And you'd need a grown-up pony to go with you," Apple Fritter said.

"My sister won't mind," Sweetie Belle assured the farm pony. "She's to busy designing dresses anyway! She won't even notice I'm gone!"

"As for the pony to go with us," Scootaloo said, "I think I know just the one."