Shining Armor and Cadence's spell reveals something completely unexpected as it expels Chrysalis and her changelings out of Canterlot: A secret kept from everypony for several years...

Now with a TV Tropes page! Warning: Will Contain spoilers.

One by one, Twilight and her friends must come to terms with the consequences of being the Elements of Harmony.

These stories take place in the intervening time between Season One and Season Two,
with the exception of Ditzy Doo: Muffins, which takes place early in Season One.

The series continues in the sequel, Secrets and Lies.

Pony Psychology has a TV Tropes Page.

Twilight Sparkle is dying. The pony body was never meant to handle her level of magic and now even the smallest spell causes her body to degrade. The only cure is to stop all magic use and hope that her body slowly heals itself, but things are rarely that simple. Celestia has fallen ill and her only hope lies in Yggdrasil, hidden deep in the Crystal Desert.

Pinkie Pie's unrequited love for Rainbow Dash reaches crisis point as she fears the party in her heart has at long last come to an end.

Illustration by the awesome Mogasaki/Swaetshrit.

Many years after sending her beloved protege to Ponyville, unease sits heavily on Princess Celestia's heart as her relationship with Twilight Sparkle seems to have cooled despite all they've accomplished together. On the advice of her sister, Celestia sets out to investigate and resolve the lost connection with her most faithful student. What does it mean to be a Faithful Student...or a Princess of the Sun?

Earned a six-star rating on Equestria Daily and featured on its very own TVTropes page!.

Humans.

Truth or myth? Ancient lost civilization or just an old pony's tale?

No pony has ever seen one, and most haven't even heard of them. But Lyra knows that these wonderful creatures are more than just old legends, and she's going to find out... and possibly drive her roommate insane in the process.

The Sequel to 'Faith and Doubt'.

It's been two months since the changeling attack and Shining's almost-wedding and much has changed. Twilight Sparkle is now an alicorn and has left Equestria to master her new powers. The sixth element of harmony, the corrupt abstract Doubt, has been reborn in his original form: Faith. He, along with Spike, have gone with Twilight as she sought to heal after the betrayal by her friends and family.

But Twilight's return to Ponyville will not be a happy one; in her absence her friends Applejack, Fluttershy, Rarity, Rainbow Dash and Pinkie Pie have been turned into alicorns themselves and the embodiments of their elements. They have seized power and now rule Equestria with iron hooves, using banned magic to turn their friends and family into zealots that obey their every command.

To save Equestria, Twilight will have to do the unthinkable: form a rebellion and declare war on her friends. But will she be willing to make the tough decisions... even if it means choosing between friendship and freedom?

Everything is bad in large doses.

Thank you to all that got this story featured!

The TVTropes page for Faith and Doubt/The Abundance can be found here: http://tvtropes.org/pmwiki/pmwiki.php/FanFic/FaithAndDoubt

Cover by the wonderful FerGarcia220!

How would things be different if Twilight had never made it to Ponyville? Twilight Sparkle finds out just how different things could be when she is forced to travel to her own past while chasing down a mystery; a plot to erase Princess Twilight Sparkle from history.

Landing in a time just weeks after the one thousandth Summer Sun Celebration, she finds a world shrouded in an eternal night, where the Elements of Harmony were never recovered. Can she fix the things that should have, but didn't happen? Or is this Equestria destined to head down a different path?

Chinese Translation by Hell Organist

Once upon a time, Spike went for a walk.

While on his walk, he was judged by an ancient alicorn, lodged with griffons, parlayed with air pirates, charmed a maiden of a mystical race, and dealt with the scourges of hate, fear, and racism while deliberately drawing the armies of myriad nations to the brink of global war.

Once upon a time, Spike went for a walk, and did all of this so that he could keep a promise to the one that meant the most to him... Twilight Sparkle.

In the first of three books, Pillars of the Sun (Chapters 1-15), Spike is devastated by Twilight's fate and grows more and more despondent as he attempts to understand what has happened to his dearest friend. A gentle nudge from a pony he trusts sends him looking for answers. When that nudge becomes a push he unravels ancient secrets... and risks losing himself before his attempt to rescue Twilight can even begin.

Be Awed and Amazed by the tale of Sweetie Belle as she traverses the multiverse in search of her lost mentor and friend, Twilight Sparkle! Will she find her in post-apocalyptic Equestria? Or maybe in a strange world where everypony is the wrong gender? Or even where a Pony claims to be a human? Read as she journeys through very familiar worlds you might have read about... if you dare!

At this point in time all the main worlds to be visited have already been chosen. Thank you all for the suggestions, and I hope you enjoy the surprises!

Here's the official TSC:F Music Intro: The Sweetie Chronicles: Fragments

WDTP: S2/3-CE
You can also visit the TV Tropes Page which has spoilers!