A wanted robber escapes the royal guards and stumbles upon Pinkie Pie, who invites the criminal into her home. But little does the criminal know, that under the pink, happy surface, lies a bloodthirsty killer. What fate will this bring upon the Mane six?

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn

Scootaloo has never talked much about herself. Nopony knows her family, or has visited her home. But she has one big secret she's never told anypony... especially Rainbow Dash.

This story is a sequel to The Rainbow's Surprise

On the day of Fluttershy and Rainbow Dash's wedding, Princess Celestia left Twilight a message saying that she should prepare herself if something happens. The next morning, Twilight awakens to find that all of Ponyville has succumb to a blinding fog. She must now travel a monster-filled town in search for her teacher and friends and try to return Ponyville back to the way it was.

A friend notices Applejack acting odd and calls her out on it. With that prodding, our honest earth pony manages to cough up the truth to Twilight and is shocked when she is eager to try out being more than friends. Knowing they cannot put telling the others that are important to them, Applejack and Twilight are quick to make the rounds and things mostly go smoothly. In the end, things look bright for everyone.

In a freak accident from the Cloudsdale weather control team, Twilight is struck down by an errant lightning bolt. But the veil of death is relatively thin...

Pinkie Pie is being tormented by horrific nightmares. Unable to deal with it by herself anymore she seeks out Twilight's help, but will it have been the best decision when she finds herself alone in an abandoned, fog filled Ponyville?

Sequel: http://www.fimfiction.net/story/4676/Too-Shy-for-a-Rainbow

There have been a LOT of high-quality readings of Silent Ponyville, but this one is my personal favorite:
https://www.youtube.com/playlist?list=PLGh01rbB4o3xoSV7a6Omc-UJROXHRZ1Hv

An unfortunate event gives Princess Celestia a fresh view on her life by forcing her to see the world from a very different viewpoint. With Equestria changing around her, she is faced with a personal crisis... if she can ignore how cute a certain lavender unicorn suddenly looks to her.

Featured on Equestria Daily!
And some site about horse porn!
Liked this story? Read the sequel.
And the story this was a sort-of prequel to.