MLP:FIM is owend by Hasbro and created by Lauren Faust, I only came up with this story line and some of the characters.
A story by Gnomeflame
In Equestria, night has covered the skies as Twilight walks the dirt path through the Everfree's to meet up with Zecora. As the happy mare trots down the pathway, she is carrying a rather big satchel with many pockets on her back. But as she trots up the little hill, she sees that something is wrong.
As she looks at Zecoras hut, one of her windows is shattered, and her door was wide open. Twilight then dropped he bags in panic, and ran to the house to check on her friend. But as she enters the house, her furniture was tipped over, her cabinets emptied with the contents spread across the floors, and several empty vials lay cracked on the floor.
But as Twilight moves into the Zecoras cauldron room, she sees her friend laying on the floor, presumed dead. She then screamed and ran out the house to get help of some kind.
12 Hours after the event
As Zecoras hut now had several Equestrian guards roaming the grounds and the interior, Doctor Whooves walks down the path with the captain of the guard.
"What in pony hell is going on around here now." "Robberies, broken property, and now murder in the very heart of Equestria."
"I don't know Captain Gold but whatever is going on, I don't like it."
As the two eventually get to the house, the guards let them by, and Doctor Whooves investigates the body of Zecora. The Captain looks around puzzled as he sees some of her belongings but then quickly runs to the doctor for info on the death.
"What are we looking at doc, who could have done this."
The doctor takes awhile to answer as he examines the body. "Well it would seem something physical didn't killed her, it would seem maybe internal or..." but he stops as he senses a pulse. "By Celestia" he said with immense shock.
"What, spit it out doc" said Captain Gold with out hesitation.
"She's alive, but there is no consciousness, it is like her soul, just left her" he said turning his head slowly to the Captain.
"That's, not possible how did this happen" he said with slight fear in his eyes.
As the doctor looks around the body, he sees a strange marking on Zecoras flank. "Look at this, it appears to be an eye of some sort" he said with puzzled eyes.
As the Captain looks down, he sees a marking of an black eye but quickly states "that's probably her Cutie mark doc" he stated to Doctor Whooves like he would if he was dumb.
"Yes captain I would have said that but, Zecora never had a Cutie mark" he said as he gazed at the mark. "But from what it appears, Zecora is in an endless sleep" he said as he started walking towards the door.
"Were in pony hell do you think your going Doc"
"Im going to try to figure out what is going on, if you need me I will be at my office"as he walks off, the captain quietly curses to himself.
2 Hours after the Doc left the scene, at Twilights house.
As Doctor Whooves walks up to Twilights door, he cautiously knocks on her door. As she opens the door he is invited in by Twilight. The Doctor walks around the house looking at her extensive collection of books.
"You sure do have a lot of books Twilight, I cant even see how you keep track of all of them" he stated trying to make small talk with Twilight.
"What are you here for doctor, I have already been asked enough questions today" she said with a slight tear in her eye.
"Im sorry Twilight, I did not mean to bother you, but I really need assistance with something."
Twilight then looked at him and stated "With what, does it have to do with, the case" she said holding back her tears.
"Well yes, I need a book on markings and what not" he said cautiously in fear he would make Twilight upset.
"Why, what does that have to do with anything that's going on" he said now crying.
"I, noticed something on Zecoras flank, it is in the shape of an eye" he said staring at Twilight.
"What, how is that possible, she never had a marking of an eye before."
"I know this, that is why I need a book for markings, I may be able to figure out a way to save her."
Then Twilight took a deep breath and started "Ok, if it will help bring back Zecora, I will get you a book on markings."
"I assure it to you Twilight, I will get your friend back."
Twilight then made a slight smile as she went over to her bookshelves and began taking books out. Then Doctor Whooves went and laid down on the floor waiting for Twilight, but as he waited he started to think.
"Poor Twilight, it must be hard losing a friend, but I swear I will save her." "Hopefully these books will help me achieve that goal."
"Drop it, if you know what's good for you" a voice interjected.
But just before Doctor Whooves could reply, Twilight came in with some books. "Here you go Doc, free of charge just save my friend" she said giving a smile to Doctor Whooves.
"I thank you Twilight, and hey if you ever need to talk, im always open" he said as he left the house.
30 Minutes later, back at the Doctors office.
As the doctor laid all his books down on his desk, he just had one question in his head.
"Who was that voice, it appeared for a second and left" he said as he stared at the books. "But no matter, it was probably just someone outside Twilights house arguing with there mate" he said with a smile.
But as he looked through the books, he eventually found a page with the eye, with a brief origin of the mark. It was said that this was the mark of a dog warlord named WolfBite who was known for his terrifying stare. He conquered many tribes before he became a threat to Equestria but the rest of the page was missing.
But as he stared at the book, he still did not know what the mark means, but he knew that I cant be good. But before he left his office to tell Twilight, he heard the voice again. "Doctor, Doctor, Doctor, why is it that you do not take my warning." "What your getting yourself into is to much for you, you still have time to evacuate the town" said the voice in a laugh.
"Who are you, show yourself" said the doctor looking around him in panic.
"Who am I, well doctor I am just a voice, but continue down your path and well, you will then know me Doctor" said the voice as if he was talking down to him.
"Are you the one behind the attacks" the Doctor asked with angered eyes.
"Who knows, maybe I am, maybe im not, but again continue down your path and I cannot guarantee your well being Doctor."
"Your empty threats do not move me one bit voice, you will never stop me from figuring out the meaning of this."
"Well then doctor, cant say I didn't warn you, welcome to the game" the voice said in a laugh as the voice faded.
As Doctor Whooves then left his office, a figure watches him from the forest.
6 a clock in the morning 10 hours past the encounter.
As Doctor Whooves gets several knocks on his door, he opens the door to reveal Captain Gold.
"What is going on Captain Gold" he asked in the usual tone when you first wake up.
"There were, kidnaping's this time Doctor" he said holding his helm revealing his gold mane.
"What, how, the town was all but asleep."
"Yes but that's not all, we found them, parts of them anyway" he replied in a sad tone.
"Why would someone do such a thing like this."
"Doc, your gonna need to follow me to the scene, there is something there that I think you are familiar with."
As the two walked through the Everfree forest, they eventually got to a tree. There were two dead mares and three dead colts with bits and pieces of them gone.
"What monsters could have done this, I once served these ponies before, nothing bad about any of them" Doctor Whooves said as he looked at the mutilated couples. But then he noticed the eye was on all there flanks. "That eye, it is the eye of WolfBite, we must hurry and find the being that is doing this" he said in a stern voice.
"Who is this WolfBite you speak of doc" he said staring at him.
"Long story short, that is his mark, whoever or whatever is doing this has a connection with WolfBite's clan." "Im going to need clearance into the Equestrian military library."
"Whoa there Doc, im just the captain of the guard, but I guess I can see what I can do in the mean time, I will have to try to spread the militia through Ponyville." "This is going to be the last time somepony dies" he said as he walked off back to Ponyville.
1 hour after the incident, Captain Gold sets up a town meeting in the town hall.
"Greetings residents of Ponyville, I Captain Gold and many of you have noticed the sudden disappearances going on lately." "Parents I advise you to not let your children outside without supervision, and I now must set a curfew for the town."
As he said this many ponies began to yell including Applejack. "Im sorry Cap, but were gonna need to work harder this season on Apple Acres, we cant have a curfew."
"I understand your frustration citizen I really do, but this is to protect everyponie from this menace."
As he said this Rarity walked up to her friend "im sorry Applejack, but its best not to argue he is right you know."
As angry as Applejack was she kept quiet for the whole meeting. As Gold finished talking everyponie went back to there homes. But as AJ walked with Rarity, she started to talk.
"Im sorry Cap, but this curfew aint gonna stop me and my boys and gals from working." "Somepony has to buck the apples this year" she replied.
But as they walked off, a figure watches them from the woods.