Author's Note
This story idea actually came to me in science class for some reason I do not know why. the letter to Celestia was the first thing to enter my head and it just expanded from there. I actually wrote the letter on my school work that I had to hand in and when I got it back the teacher had wrote down "what" with a confused face on it. 
Anyways I hope the story will come out good and I hope you will all enjoy the story. If you are interested you can check out my first story What's With Fluttershy.
Also please no mean comments, I like suggestions and all but nothing rude and hateful
Dear Princess Celestia
Princess Celestia came walking through the doors to her royal courters with a letter enveloped in a light yellow aura which was her magic. Celesta shut the door behind her with her back right hoof and took a seat on her large pillow in the center of her courters and opened up the letter to read it.
Dear Princess Celestia,
I do not know what I should do, before I was reformed I corrupted the mane 6 to act the opposite of their true self's. But when I was reformed I realized that my friend Fluttershy still has that corrupted part in her somewhere so I decided to remove it and lock it up somewhere I thought it could never escape,( the place were cancelled out magic goes). But she has, and now will and can endanger everypony. I don't want to hurt neither one of the two Fluttershys. I don't know how but I WILL stop this alternate Fluttershy and fix everything, no matter how long it will take, I promise.
Sincerely, Discord
Princess Celestia put down the letter with a worried look on her face." Oh no." Celestia mumbled to herself.
Down the castle halls Luna was looking for her sister. "Tia! Tia! Where art thou!"
" Your majesty." Luna turned around to see one of Celestia's royal guards behind her. "If you are looking for your sister she is in her room. She wanted some quiet while she handled some of her duties. "O.K. we thank you for your information." Luna responded to the guard with a smile and a nod right before she went to her sisters room to talk to her.
" Sister, Is thou alright we heard mumbling is there a problem that we can solve." Luna asked as she entered her sisters room with a concerned look on her face" No dear sister it's nothing, I just..., no never mind it's fine." "Very well then." Said Luna as she started to walk out of Celestia's courters and over to her own just down the hall, but with the thought in her head 'then we will have find out for our-self.'
As Celestia saw her dear sister leave she felt a bit of guilt for not telling Luna what was wrong or even what was in that letter for that matter but if she knows Luna, then she knows Luna knew something was wrong would stop at nothing to find out what was wrong even if it took all eternity.' Maby I should have told her.' Celestia finally thought but then again Luna is a smart pony she would probably find out eventually.
Author's Note
Hi everypony, I do realize that this chapter is on the weaker side 
but once evil Fluttrshy comes in it ill get a lot more thrilling and better over all, I pinkie promise. Cross my heart, hope to fly, stick a cupcake in my eye.
The Night Before part 1
Discord was on his way to Fluttershy's to help out with the animals as he entered the gate to her cottage. "KNOCK, KNOCK!" "I will be there in a second." Fluttershy responded to whoever was on the other side of the door in her soft sweet voice but projected just a little so it can be heard from a far distance.
Fluttershy began to trot to the front door until she was in front of it and turned the knob with her hoof. " Oh hello Discord, what brings you here this late?" Asked Fluttershy with a smile. "Well..." Began Discord. "I was bored and was wondering if you needed any help with your animals?"
"I don't know Discord I already tucked all the animals in and the nocturnal ones are already taken care of as well. Besides I have been a little cranky from how early I got up and now how late it is getting now." Discord held his head down from hearing what Fluttershy just said everypony else was fast asleep and Celestia and Luna were to busy, who was he to spend time with. When Discord turned back to Fluttershy he got this negative vibe from her, not just any vibe though, a vibe that he created.
"Uhh... Fluttershy? Can I run a small little test on you?" 'Man that sounded bad.' Discord thought to himself and what was worse is that he just spat it out. Discord could not have made what he just did any worse.
"Huh?" Was all Fluttershy could say in return. "I am just getting a negative vibe from you and I want to find out what it is from." For some reason Discord thought that he said that the wrong way. Fluttershy now felt unsettled by what Discord said and in a way had a strange urge to yell at him. "Umm...Discord I think you should leave you are kinda making me feel uncomfortable."
'I new it.' Discord thought to himself, he could not have just come up with a better way to put it in fact anyway could have been better. "Alright I will let you relax. Sorry." Discord said as he came up to Fluttershy and gave her a goodbye hug, but as he did he put a small device on her back that would measure any dark or chaotic magic that could still be in Fluttershy since her corruption.(being that was their real first encounter together.)
The two of them said their goodbyes and Discord vanished in a bright flash with Fluttershy still there with no idea about the device on her back.
In Discords home
"Now to check in on my dear friend Fluttershy." Discord said to himself as he took out another device but this one was the main one and far more bigger, it gave out all the info that was being collected by the other device currently on Fluttershy's back.
Discord took a hard, long look at the small screen on the device. "Oh, No!" Discord said as he looked up from the screen.
