Chapter 1
"Fascinating!" said Twilight, jotting notes in her journal as the potion she was working on hissed and spat purple sparks under the influence of her magic.
Twilight's magic flared brighter as she concentrated and the potion responded by glowing a deep shade of purple and bubbling violently.
Somepony chose that moment to knock on the door. Twilight glanced at the door, then turned back to the potion quickly as it began smoking. She quickly tried to use her magic to fix it, but it was too late. The potion burst into flames before exploding in her face.
Wiping ash off her face, Twilight went to the door. "Yes?" She asked irritatedly, opening the door.
Twilight look around "Hello?" She asked, but there was nopony around.
She was about to close the door and go remake her potion when she glanced down.
"What's this?" She wondered, picking up the scroll that was on her doorstep.
She closed the door and walked to her desk, opening the scroll as she did so.
Twilight
I'm afraid I have a matter of grave importance to discuss with you. if convenient, please meet me at Sugar Cube Corner at precisely 7 o'clock this evening. Please do not tell anypony else that you are coming.
Twilight flipped the note over, wondering if there was anymore and read If inconvenient, come anyway
In place of a signature there was a picture of three balloons shaped very much like the cutie mark of a certain pink earth pony.
Twilight set down the note and looked back up at the clock. It was half past three.
Well that's when I was planning on writing my friendship report to Princess Celestia Twilight thought to herself, summoning her schedule.
Maybe if I start that an hour earlier- No, then I won't have time to get Spike's 7 hour bubble bath ready The purple unicorn began writing things down, then scratching them out with a shake of her head, trying to fit a meeting with Pinkie Pie into her schedule.
"I wonder what Pinkie wants" Twilight wondered aloud as she walked slowly to Sugar Cube Corner.
Twilight was a little cross. She had finally managed to fix her schedule so that she could meet Pinkie, but as soon as she did, the clock had struck 7.
Twilight wondered if it was even worth meeting Pinkie, considering all the important things she still had to get done. But she had already reached Sugar Cube Corner, so she decided to find out what Pinkie wanted.
"Hi Pinkie!" Said Twilight, pushing open the door and seeing the pink pony sitting at a table.
"Twilight!" Exclaimed Pinkie, bouncing up and bounding over to Twilight "I'm so glad you're here! I mean, I was worried for a little bit because it passed 7 and you're usually so punctual and I thought you weren't coming but now you're here and-"
"Pinkie, I hate to be rude, but I kind of have other things I need to do, so could you please just tell me what you wanted to talk about?"
"Cupcakes!" Exclaimed Pinkie, producing one from nowhere.
"Cupcakes?" Asked Twilight "That's what's so important!?"
Pinkie nodded a few times and held out the cupcake to her "Here, try it!"
Twilight sighed and decided to just try the cupcake and leave.
"Pinkie," she began as she took a bite of the cupcake "I thought you said the matter was of grave importance."
"Oh it is Twilight!" Said Pinkie earnestly as Twilight finished the cupcake.
"Then can you explain how a cupcake-" she suddenly stopped as a wave of dizziness washed over her. "Can you ex-" the world started spinning and she felt to the ground.
"Its a matter of your GRAVE importance! Ooh, that was a good one!" Pinkie giggled as Twilight faded into unconsciousness.
Twilight slowly regained consciousness some time later.
As she opened her eyes, the first thing she registered was searing light. She shut her eyes quickly and tried to will the spots away from her vision.
"Oh look girls, Twilight's awake!" Twilight heard Pinkie say.
Twilight ignored Pinkie and explored her situation with her other senses. She was lying with her back on what felt like a metal table. She was held in place by what felt like leather straps on her legs. She could also smell a very faint coppery smell, suspiciously like dried blood.
Finally, she decided that was all she could figure out without opening her eyes. Slowly, she opened her eyes a crack.
"Hiya Twilight!" Said Pinkie Pie, who was standing in front of Twilight, back lit by a bright light. "We were all wondering when you'd wake up!"
"Pinkie Pie, what is going on?" Asked Twilight, squinting in the harsh light.
"You're here to help me!" Said Pinkie "Well, you're here to help US." She amended "Come on out girls!"
Twilight watched as 5 ponies stepped into the light "Rarity! Rainbow Dash! Applejack, Fluttershy! Help me! Pinkie's gone crazy!" Twilight shouted once she recognized the ponies. The last pony was barely in the light though, so Twilight couldn't tell who it was.
Pinkie just giggled "Oh Twilight, don't worry, I just want to talk! You see, I'm not really who I say I am!"
Twilight looked at her in confusion "What do you mean Pinkie?"
Twilight watched as Pinkie reached into her mane and began unzipping a near invisible zipper. Twilight gasped as the Pinkie Pie suit fell away to reveal...
Pinkie Pie?
"Pinkie Pie, that's a very realistic, umm, disguise, but what-"
"Oh Twilight, I thought you would have figured it out by now!" Said Pinkie, cutting Twilight off "Don't you remember the mirror pond?"
Twilight thought back "Yes, but what-"
"You sent all the mes back into it! And it's soooo lonely being in a pond! I couldn't let you sentence the poor mes to that fate!"
"You don't mean-" began Twilight
"I knew you were smart Twilight!" Exclaimed Pinkie Pie as Twilight's 4 other 'friends' unzipped themselves to reveal 4 more Pinkie Pies.
"Pinkie Pie, what is going on? Why are you all disguised as our friends?"
"We're not dressed as OUR friends" said Pinkie "We're dressed as your friends!" At this, the other 4 Pinkie's nodded "You see, all of you," continued Pinkie "wanted to get rid of us, which made us soooo sad! I mean, all we wanted to do was have fun! Even Pinkie here wanted to get rid of us." Said Pinkie, nudging the Pinkie suit at her feet "So we came up with a way we could stay here and have fun!" She finished, bouncing with excitement.
"Pinkie Pie" said Twilight nervously "You can't mean-"
"Oh but she does!" Said the Fluttershy Pinkie.
"We decided to replace you!" The Applejack Pinkie said with a smile.
"These body suits are so fashionable-" began the Rarity Pinkie.
"That they make us twenty percent cooler!" Finished the Rainbow Dash Pinkie.
"And now its my turn!" Cried the fifth pony, jumping into the light to reveal yet another Pinkie.
"Pinkies, you're crazy!" Shouted Twilight, tugging at the straps.
"We're not crazy!" Said all but the Pinkie Pinkie in unison, pulling out razor sharp medical scalpels and advancing on the struggling Twilight "We're Pinkie!"
"Remember girls, keep her intact or we can't use her!" Said the Pinkie Pinkie, watching as the other five descended on the struggling Twilight like piranhas.
"Oh, this is going to be so much fun!" Exclaimed the last Pinkie as she made the first incision, adding Twilight's screams to the shouts of "Fun! Fun! Fun!" From the other Pinkies
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Well, that was unreasonably terrifying ...
3976760 It's so strange! Everypony keeps saying that!
I can't imagine why...
3976765 Well, for me, it's the idea of the identical fleshsuits. That sort of thing creeps me out.
well after season three its a new way to look at the cupcake story, use the flesh for suits and the meat in the cupcakes.....the whole town could be nothing but pinkies in suits
I almost thought you were going for another cupcakes for a moment, I was about to dislike the hell out of this!
Good thing I kept reading!
*jaw hits floor* Wud?
3977122 Hey, me neither!
3977849 Yay for continuing to read!
3978338 I can't tell if that's a good sign or bad sign. You should probably see a doctor if your jaw tends to do that though.
3978363 I was suprised
You got me there! So relived. I've seen cupcakes... I don't wanna talk about that
Thank god it wasn't that. Another lesson for me to learn; don't judge a book by its cover. In this case, don't judge a STORY by its TITTLE! Love it, hope you write more stories like this!!! 
3991817 Aww, thanks!
I've actually written another story inspired by this (sorta) but it's kind of sick and I'm debating whether to publish it or not
Well, that realy
dumb.weird
3995661 *was really
Thank you for your valuable insight on how I can improve my writing style
3995959
I just had a lack of anything else to comment =P
Is "I like muffins." a relevant comment? No? Well okay then
There's another story that's kind of like cupcakes called "The End of the Rainbow" and the author split it in two stories. The first story told everything that happened and the ending after it happened. The second story said the same things, except it also showed the part where RD is being tortured and killed. I think it would be cool if you could make a second story, or another chapter, that people can read if they want to know what happens to Twilight. Just a suggestion. But this was really cool!
3991857 You should! My favorite genre of mlp fanfic is (especially all combined into one story): Sad, Dark, Tragedy. I don't know why I like these, but I just do...
3999638 I need to make it longer, apparently I'm like 100 words short
But yeah, I'll probably upload it if I can make it longer
Keep an eye out, I'll probably upload it later this week. Sooner if I decide sleep is for the weak again
3999648 Wait, there's a limit for how short your story can be?
I didn't know...
3999708 1000 words or longer or you can't publish it
3999716 Well that makes me feel better when (or if) I publish a story, because I love and feel like i need to write long stories.
I... Holy fuck, excuse my language, that was something else. Here I think the fast pacing went well and ended with my eyes widening in realization and horror at what was happening. Great story, I loved the end! Haha. It comes to show that you don't need a lot of details or experience to write really good fics. (That is not to sound rude...) I really liked this. Good job. The beginning started off a bit too fast, but it quickly smoothed out as it continued. Finally that end... Damn... It's like the freaking body snatchers, but pony style. Soon the whole of Equestria will be replaced by Pinkie Pies... XD
4009259 Haha, I'm glad that you enjoyed it
Found a spelling error
~
Your friend,
Trade Jack
Well I'm glad Cupcakes inspired you. This fic, in my opinion, was great, and I hope you continue to write and perfect your craft.
4062884 Wow, thanks. I'm glad you enjoyed it!
Woah! Awesome story!
4400231 Thanks!
I gotta say it sure was different. Im glad i read it
........AAAAAAAAAUUUUUUUUGGGGGGGGHHHHHHHH!!!!!!!! But seriously, this story is actually really terrifying to me. Not that I hate it, I like it a lot, but I think this to be more horrifying than Cupcakes! I mean, the very thought that something like this could happen,is bone-chillingly frightening, wouldn't you say? I thought I was paranoid before, now I'm scared that something just like what happened to Twilight in this story might happen to EVERYBODY. ON. EARTH! Yeah, thanks for the Nightmare Fuel. I really appreciate it.
4504483 You're welcome friend!
Intersesting...
But you should've added more..
PLZ DO SO
I was expecting a dark comedy, given the comic for the cover image.
Damn, that got quite dark. And not in the comedy way either. Just... wow.
But I found myself enjoying this, strangely enough. Hmm... upvote and move on.
O_O *runs all the way back to manehattten* I SAW NOTHING!
4724223 Upvote and never look back!
That was... what the Hell was that?! In any case, I think I liked it... whatever it was... upvote, favorite, and meds to come...
5613133 It turned out a lot darker then I had originally planned when I came up with the idea, haha. Glad you think you liked it at any rate
5613145 I run a reviewing comedy show, so if I ever have an episode about one-and-done stories, this is going to get some praise in it!
5613155 Really?
Omigoshomigoshomigoshomigosh! 
5613886 Indeed! It may be a while, I'm currently having both a theme month for Applejack AND a 20 Follower special where I have to review the worst story ever made. But, as soon as both of them are done, I'm going to make the one-shot episode!
5614151 *fangirling intensifies*
it was a little scary, but all in all I'm happy that those pinkies can live, on the one hand I'm sorry for the fate of the mane six, but on the other .. .. ..
fun, fun, fun, fun, fun, fun
Pinkies conquest the world
I'm undecided between cheering for the pinkies that invade the world ......... and perhaps the multiverse
or be sorry for the other inhabitants of equestria
anyway ......... live pinkie