Old Verison of Story (I'm rewriting all chapters.)
Author's Note
This is the old version of the story. I'm currently reworking the entire story to make more sense. There were plot holes and opportunities I missed while writing this. I plan on making it better. I know more now than I did one year ago. I want to thank FanOfMostEverything for writing a great review that showed me a lot and gave me the motivation to start writing again. If you want to read the fantastic rage review on this then here it is: http://www.fimfiction.net/group/201778/rage-reviews/thread/203418/rage-review-secret-agent-derpy
Old Verison of Story (I'm rewriting all chapters.)
Derpy's Day Off
It was a bright and sunny day in Equestria and it was Derpy's favorite day of the week because she didn't have to work. She liked her job as a mail mare but not as much as she liked muffins. She was flying to Sugarcube Corner because today is the day, Mr. and Mrs. Cake make a special muffin just for Derpy. The sweet, fresh baked muffin smell flowing through and hugging her nose ever so gently sends her mind into a frenzy of joy and hunger while slowly making her mouth water.
As Derpy walked into Sugarcube, she was greeted by Mr. Cake. "Well, hello there Derpy, here for the special?" Mr. Cake announced. Mr. Cake pulled out a tray containing 3 mouth-watering muffins.
Derpy yelled, "Yay muffins" and a smile came across Derpy's face so quick that the shear force could break the sound barrier as those sweet muffins came into view. The smell was filling the room as Derpy smiled like a mad mare and her wings opened up and started shaking from the pure, sweet joy coursing through her. She started speeding towards them, knocking a couple ponies off their hooves as well. She focused on those muffins and nothing else mattered to her. She grabbed the muffins, and sped out the door in a flash.
Derpy raced home and all the doors and windows locked as if set automatically. She plopped down, almost breaking the chair in the process, and slammed the muffins on the table. Derpy inched the muffin towards her mouth, slowly taking in the warm sweet smell as it drew closer. By this point, Derpy's mouth was watering like a raging river. Derpy was just about to put one in her mouth when she heard a sound at her door. "Knock! Knock! Knock!" pushed into her ears, as if pleading for help and demanding an answer like they were at war. Derpy froze, eyes turned a shade of crimson, steam shooting from her ears as rage slowly cuddled with her thoughts and tickled her mind. Derpy jumped up and flew towards the door as quick as lightning.
Once Derpy had opened the door, she was greeted by a hoof knocking on her face while Twilight was saying, "But Spike we need to find....," Twilight paused to realize she made a horrible mistake. Derpy winced in pain and tears flowed down her muzzle as she was rubbing her face. "I'm so sorry Derpy. You're not hurt, are you?" Twilight asked in a panic. Twilight's wing flipped over Derpy and hugged her side. Spike hit the floor and laughed so loud that it woke up Luna in Canterlot.
Twilight turned to Derpy, "Have you heard anything from Celestia recently? She hasn't answered any of my letters for weeks now." Twilight looked worried as tears started forming in her eyes.
Derpy wrapped her wing around Twilight and said, "No, but I can head over to Canterlot to see why Celestia is not answering." Twilight slowly smiled and said, "Thank you Derpy." Twilight lit up her horn and encased Spike in magic and dragged Spike along the ground as she turned to leave. Derpy slid the door closed, then she packed up her muffins.
She packed her bags and flew towards Canterlot as fast as she could.
Arrived In Canterlot
Derpy arrived at Canterlot Castle and flew towards the throne room. "Security was tight around the castle," Derpy thought as she flew through the halls. Throne doors slammed open. Derpy's mouth gaped open and her eyes slowly became the size of watermelons. "Why sister?" cried Luna as tears flowed down her beautiful coat. Cobwebs were working to claim Celestia's throne, as Luna's tears fought back the horrible cobweb menace.
Princess Luna and Derpy have been best friends for a long time due to the fact that, Derpy has time to talk in-between delivering mail to each pony everyday. Luna was always Derpy's favorite mare to see during her daily route. Luna would always give Derpy a smile and be so nice to her.
Derpy ran to Luna to say hello but then Derpy saw how sad Luna was and decided on a hug instead. Derpy hugged Luna and then Luna told Derpy what the problem was. Luna knew she could trust Derpy with anything and Derpy would always be willing to listen.
"I can't find my sister anywhere." cried Luna with tears in her eyes and her hooves still around Derpy tightly. "No pony has seen her in two weeks."
Derpy knew something bad must have happened if Luna was this upset. Derpy held Luna in her hooves for a while to comfort her so she could calm down.
After Luna had calmed down, they both decided to go check Celestia's room together. The door to Celestia's room was shut tight and Derpy couldn't open it on her own. Luckily, Luna was by her side helping her.
They bust through the door and look inside to find these green pods before them. It looked like there were guards inside and each one had a green googly eyes. Derpy waved a hoof in front of one and got no response. Luna looked around but found no sign of Celestia.
Luna said in a sad tone, "she isn't here."
Derpy nodded in agreement, "We need Twilight."
Luna look at Derpy, "Twilight?"
Derpy jumped on Luna's back and pointed forward, "to Ponyville."
Luna looked puzzled for a moment but then opened her wings and flew off to Ponyville.
Rise Of The Chrysalis
Meanwhile...
A changeling quickly rushes in and bows before a throne, "My queen, they have found the pods hidden in Celestia's room."
Queen Chrysalis opened her eyes and said, "Perfect" while giving a evil grin. "You hear that Celestia, Someone found the few presents I left behind. Isn't that wonderful?"
Celestia frowned as she tried pulling her hooves out of the sticky goo but to no avail. Celestia said, "Twilight will stop you even if I can't!"
Celestia's mane was suddenly pushed backwards by a massive gust of wind and green flames as Queen Chrysalis focused her horn's magic. Rage engulfed Queen Chrysalis's eyes with an eerie green glow and the same green glow pulsing up her horn. Queen Chrysalis said, "Twilight won't do anything when I am through with you and how dare you use that name in front of me." Queen Chrysalis's horn shooting magic at Celestia's horn with blinding speed while laughing madly like a mad mare.
Pain shot through Celestia's body like an earthquake and her thoughts slowly faded and became harder to form. Tears flowed down her face as quick as a bullet train. Magic traveling through Celestia's horn then breaking through her skull and attacking her brain. Celestia's eyes flew around and around in circles until they were pure green. The last bit of herself faded as she was unable to keep up the fight for control. She was now but a mere puppet for Chrysalis to control.
Queen Chrysalis smiled as Celestia fell to her power. Queen Chrysalis said, "Now no pony in equestria can stop me." Queen Chrysalis turned to her changeling and pointed her hoof to the door and said, "go and report back if anything else happens."
(Unreleased and unfinished) Gloom Day For Equestria
Derpy and Luna arrive in Ponyville and decide to rest up for the night before trying to find Twilight. Luna raises the moon and they both head off to Derpy's house to sleep for the night.
Once they reach Derpy's house, Derpy unpacks a muffin and shares it with Princess Luna and they both head off to bed.
The sun was blazing hot over the land of Equestria but the day could only get darker from there. If only the ponies below knew how true that it would become.
Derpy stopped in the middle of the white, clean hall of the Ponyville Post Office and stared out the window at her reflection. “I’ve been working too hard lately. If I work any harder than I’ll look as old as Applejack’s Granny Smith.” she said with a sigh. Suddenly her reflection looked like it was trying to talk to her. She shook her head and galloped as fast as her hooves could carry her. The reflection’s eyes followed her as she disappeared from view and then turned to walk away.
Knock!
Knock!
Knock!
“Come in” said her boss through the door.
“Boss, could I take the day off?” asked Derpy as she walked into her boss’s office.
“Well… I hate to lose one of my best workers. Although, we don’t have a whole lot going on ever since the bad news in Canterlot. You know, that damn princess ban on mail during a time of danger is really hindering my business. So I guess I can let you go for now but I want you back here in the morning.” said Jeff Paper, a very athletic purple stallion with a big bushy beard that covered his muzzle and a ten gallon hat atop his mane.
Her face lit up with joy and said, “Thank you Jeff.” She flew towards him and gave him a bear hug before shooting out towards the door. Her stomach growled at her as she smiled.
Author's Note
I made the prologue to mainly show a glimpse of what her workplace and boss are like. It is better than Derpy just having a day off every week like my past self wrote.
She works long hours and overtime so she would be very proud of herself. 
Hopefully you enjoyed the prologue. I've debated the idea of the prologue for a while now. I finally decided to release it. I'm sure this will deepen the plot later on. 
If you didn't enjoy then I hope I, at least, improved.
