In an effort to keep her mind occupied, Twilight Sparkle decides to delve once again into the grand mysteries of Pinkie Pie. This time, Twilight's focus is on her claims of growing up on a rock farm: like so many things related to Pinkie Pie, the idea that somepony could grow rocks as an agricultural product makes absolutely no sense. However, the investigation eventually leads Twilight to a rather... surprising discovery.

This is the first story in The Petriculture Cycle.

Artwork by Page Turner. Now with a TV Tropes page.

"Suppose I killed them all?"

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...

Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

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 is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim

What started out as a beautiful celebration for a dear friend quickly goes wrong. Friendships that were bonded stronger than steel have been shattered thanks to a fight, leaving one little girl heartbroken. When a whsh upon a magic stone transports the former allies into a strange new land, Twilight, and Rainbow Dash help them in their situation, but an old threat forces them to work together to save Ponyville.

This is episode 1 of the 8-part MLP X Sonic the Hedgehog epic series. Follow their adventures through Equestria as they try to bring harmony to Ponyville and themselves.

Reading an epic tale of one of the Third Hokage's missions, a 6 year old Naruto sets himself on getting some awesome summons of his own. Unable to find a contract on short notice, and not understanding why a contract is required, he goes through the necessary motions anyways and winds up in Equestria. Can Naruto convince the locals to let him be their summoner? Is the ninja world ready for the likes of Pinky Pie? Just how much will a young Naruto benefit from the Magic of Friendship?

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!

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?