The Doctor visits Equestria on a randomized 'vacation,' picked by the TARDIS. However, it turns out to be more than he counted on, as he must overcome some old enemies, and save not only Equestria, but history as he knows it.

The Sequel to Number 12.
The Doctor and Twilight leap into the future, though it may be a far darker place than they envision. In the mean time somehow the Doctor keeps crashing around Ponyville, something to do with Fluttershy, but what?

Rarity is startled to find her sister may not be who she thinks she is. Don't worry, there's a happy ending!! (Short)

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

To anyone who wishes to read this,this fic was meant for the enjoyment of myself and a few friends throughout the fandom. It heavily references Ponnychan, Fimchan 4chan, and various other boards that have pony related content, and contains many grimdark elements. Any vicarious enjoyment is welcome, but keep in mind it's OC and not to be taken seriously.

Squeak lives in The OC, a place where ideas are real. Ideas concerning one thing in particular, My Little Pony: Friendship is Magic. In this world, where imaginings are given form, and everything is pony themed, life isn't quite as 'Love and Tolerance' as you'd think. When a murder takes place, it launches a series of events going deeper than anypony could imagine.

A blue box has fallen out of the sky, and crashed right into Twilight's Library! A strange brown stallion, calling himself the Doctor stumbles out. Soon after, strange stone Pegasus are everywhere, one of resident weather ponies has vanished, and Twilight is tossed in the middle! The Doctor and Twilight have to find out what's going on, before it's too late!

When Bon-bon mysteriously shows up at Lyra's house in hysterics, it's up to the mint-colored unicorn to make things right. But after reflecting on their relationship, her feelings, and discovering shocking news, she discovers within herself the power to finally do the one thing she's always wanted to do.

Just a very short story with an ending open to interpretation. I may make a sequel of sorts if it gains any popularity.

Spike is curious about other dragons, and so he turns to Twilight for a lesson. She's got just the thing he needs - a book on dragons, of course!

Princess Luna has been kidnapped, along with 5 particular ponies from Ponyville! Princess Celestia is a wreck and it's up to Twilight Sparkle and her dragon friend Spike to get to the bottom of whats going on. Just because something's not there, doesn't mean it can't hurt you.

- Act I - Act II (You are here) - Act III

Twilight Sparkle has been forced upon a revelation. The life she thought she had is not real. Her memories are deceptive.

As Twilight tries to establish a hold on her new life, she realizes that her actions have consequences, even if she doesn't remember those actions. An embittered stallion eager for revenge against Twilight tells his story, and Twilight realizes just how precarious her situation is.

Meanwhile, and a world apart, a group of six ponies led by another Twilight Sparkle desperately search for a way to rescue their friend before her identity gets her killed. Rainbow Dash uncovers clues about her counterpart's past in the form of an old friend.

The appearance of an enigmatic mare with unknown motives threatens to complicate the rescue plan and warns that the interaction between the two worlds is more than anypony initially thought, for plans have already been set into motion.

Act I can be found here: http://fimfiction.net/story/92
Act III can be found here: http://fimfiction.net/story/5197