Queen Chrysalis' cover was perfect. She had removed the two ponies who could interfere, but after they show up at the wedding, can she keep her plans together?

A bit of an alternate ending. It is very similar to the finale, but a different lead up.

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.

In an alternate reality, Discord found his love of chaos came in handy for babysitting young foals. For two thousand years, since he and the princess' were kids, he's babysat nearly everyone in Equestria. Now he's babysitting the cutie mark crusaders, and while he does he recounts with them his many babysitting jobs of your favorite characters as fillies, one by one.

Fluttershy is wondering why her friends have been acting oddly around her. Meanwhile, the rest of the Mane six are at a loss as to how to deal with her.

A wicked and twisted mare, who was a friend of all ponies of Ponyville, overthrows Princess Celestia and Luna with raw power and brute force. Using dark and evil magics, she drained the magic from the Princesses to keep them powerless and imprisoned them deep within the palace, which she took the liberty of redecorating. Under this mare's reign, Equestria is dangerous, and ponies must work to retrieve resources for her research, or become imprisoned until they die of starvation or dehydration (Their bodies being used for research).

Across Equestria, rebel groups hide from the new ruler; however, a particular group of five, known as The Elements, who are admired by all other rebels for their bravery and skill, push further and harder, preparing for the day to return Equestria to its glorious, harmonious state. But as they proceed further, chances of success become slim, as the ruler cracks down on the rebel groups and begins heavily funding new ways to track them down and eliminate them. Will The Elements be able to save Equestria in time, before they're found and killed?

[Edit]: Credit for cover art to ObstreperousSynapse. Many thanks for the cover!
http://obstreperoussynapse.deviantart.com/

Fluttershy has always been pushed around it seems. Her pet bullies her into feeding him more, her friends ignore her, and nopony respects her opinions. And she is tired of it. On a particularly bad day she is given the chance to have what she wants most. To have ponies do as she says and not the other way around. But is she going to be satisfied with just that or will the power corrupt her? Who will save Ponyville from the tyranny of a mad mare? Who will save Fluttershy from herself? Who wil get Angel his lunch? *Warning. This fic contains a crying Fluttershy. Not for the faint of heart. I also do not own the picture, artist credit goes to aeroytechyon-X.

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.

One summer morning, young Princess Celestia meets a draconequus named Discord. Their lives are forever intertwined and they live out the centuries in various states of friendship and animosity. Rated Teen for violent deaths of OCs

Ebony, a gothic unicorn studying in Canterlot, is just as Satan made her: beautiful and perfect in every Way (geddit?). Join her as she lives and loves alongside her fellow goths, fends off preps, and struggles to reconcile her feelings for her two best friends.

There's also some claptrap about a hospital, but don't pay attention to that.

Pinkie Pie, secretly traumatized by her parents sending her away (by suggesting it over and over while she is sleeping) becomes deeply paranoid her friends will leave her.(Either by choice or through something happening to them.) She decides to invite them to a special party, where she will get them to stay with her, safe, forever.

Twilight Sparkle, Rainbow Dash,Applejack,Fluttershy,Rarity, and Spike must try to figure out what's wrong. But will it be too late to help anypony? And who really is in the most danger, them or Pinkie Pie.