Twilight Sparkle is having reoccurring nightmares. Then after some strange things happen one night, Twilight is called up to Canterlot by the Princess for a special assignment.

This story is a sequel to What Have You Done?

Chrysalis, the Changeling Queen, has taken her prize, unhindered by Equestria's precious heroes. Celestia is little more than another prisoner of war now. The Bearers of the Elements of Harmony are lost, and the Elements themselves have turned away from Equestria's plight. As the world they once knew begins to crumble, a single question is asked among the people as they look up at their fallen heroes.

There is no such thing as "miserably ever after," for someone will always be fighting for things to change. Hope doesn't die just because someone's turned off the lights. Truth doesn't vanish when deceit begins its reign, and Harmony can only shine brighter among chaos.
Even as this world falls, we'll work to build it up again.
Even as you lose yourself, you can find greater things within you.
Even as fear rises up like a tidal wave, we'll forge a sanctuary to stand against it.
Even as you break, someone will always be standing there next to you to carry you through it.

Cover art is by Odin-odin.
Story theme (Equestria in Grey) is by Omnipony.
Main Characters are Twilight, Velvet, Discord, Nightlight, Luna, and Chrysalis, in that order.
See you in the comments, my dear readers.

This story is a sequel to Celestia's Tiny Student

(Title changed from "Ponyville's Tiny Librarian" for reason pointed in this blog )

Twilight Sparkle is a one-kilogram pony the size of a large rat, shrunken by Princess Celestia following her entrance exam to the Celestia’s School for Gifted Unicorns to ensure that her power surges would not pose a danger to the ponies around her.

She’s spent thirteen years full of hard training at her new size, facing the life-threatening experiences that came with living in a world of giants. To survive those thirteen years of hardship and joy, of learning and adventure, and of pride and humility, Twilight has challenged herself to be stronger, to overcome any obstacle.

Now that tiny Twilight is on her way to Ponyville to oversee the preparations for the Summer Sun Celebration, how well will this miniature mare fare outside of the confines of the castle? How will the other Element Bearers react to her? How will Nightmare Moon react to the tiny unicorn? Is Twiny prepared to face Ponyville, and, more importantly, is Ponyville prepared to face her?

Credits:
Art cover - kc day

Top editors: (editing and rewritting for months, hope quality is to your liking).
Kydois
Georg

Nightmare Moon's sentences editor:
Bahatumay

Applejack accent editor:
Crimson Star (Chapter 1 - Applejack)
Rebel Brony
The Notebook is grounded

Pinkie sentence's editor:
Plump it UP

Other editors:
Hereward
tana1100
Lab (small editing from prologue to chapter 4)

Pre-reader:
Rated Ponystar

To celebrate the release of this sequel, I created a group called “Twinyverse” for all fans of this story where you can talk about it and track all side stories with ease.
The Twinyverse Group

This Story undergoing Rewrite

A freak accident leaves Princess Twilight Sparkle blind. With magic unable to help her see again she is resigned to her fate as a shadow of her former self.

Sadness and depression strike hard and fast nearly every day. But luckily for the disable princess, she may stumble across an organisation that could help her to see again. But miracles don't come freely, fortunately, she may have a guardian watching over her.

:: ORIGINAL VERSION FEATURED 9/6/2014::

My name is Twilight Sparkle.
I am three hundred and seventy five years old.
Except for Spike, all my friends are dead...But not for long

Betrayed by Celestia, and isolated in her castle with only Spike for support, Twilight Sparkle enacts a powerful spell to reincarnate the element bearers through her own body.
Her friends will be reborn, and, with the trials of being a mother to her friends ahead of her, an unraveling secret from the past following her at every turn, and the possibility of a brand new life so close in reach, Twilight just might be reborn too.

Credit for both the inspiration for this story and cover picture go to
Crystal Leviathan

After discovering that Cadence is not who she appears to be, Twilight is sent to another world entirely by the disguised Changeling Queen to avoid her plan being disrupted.
When Twilight lands, she discovers that not only have Spike, Owlowiscious and Peewee followed her, but that they've arrived in a world where the main sentient species is human.
There's still a place where they teach magic, though.
Crossover with Harry Potter. Twilight will be effectively taking the role of Hermione.

I've marked this story as cancelled to reflect the unlikelihood of it continuing. If I do come back to it I'll revert that.

Twilight gets killed protecting Princess Celestia and wakes up to the words Game Over floating in front of her.

No knowledge of TRON is necessary to enjoy the story.

Ten years after Celestia disappeared with no warning nor trace, Twilight Sparkle receives a message from the lost princess calling for help. When Twilight and Rainbow speed to Canterlot, Dash is accidentally transported to a strange world – but in her race to escape the System, she faces an enemy she never expected.

Cover art by Maxiima and RBDash47

Spanish translation by Spaniard Kiwi

Luna and Celestia's rule have come to an end as predicted by the themselves. They willingly and happily took the gift of rest after teaching and ensuring that Twilight knows how to rule.

As the new leader of the land, she spent her time filling out papers and tending to her royal duty, such as raising and lowing the sun and moon, thus depriving her of time with her friends. Her magic skills have surpassed both princesses combined already. Equestria loves it's new ruler. There is not one pony that detests her. Twilight has brought peace and harmony to the land.

Though. Even the happiest and most beloved leaders face hardship. Here is The Princess Twilight Sparkle's story as ruler. Beginning from her first day.