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.

Have you ever woken up as a vegetarian cartoon pony? I have, and she won’t shut up about it. I’m stuck in her body as our minds swap control and our memories blur. I can’t seem to do anything right, and it’s even worse when she’s in charge.

Now, we’re in a back and forth war for control of her body. I just want to eat meat again, and have a little personal space. She’s convinced I’m hitting on her friends and trying to score. I’m not sure I can survive the rest of the day, let alone until we fix this.

Edits by: Selbi, Abcron, Breath of Plagues, Refro, Jaestring, The Parasprite, Starbound Gurren
Pre-read by: SkeeterTL, Solidfire, Penjacker, TypewriterError, Pearple Prose
(It took all of them to corral my insanity.)
Cover art by Tsitra360
V1.1-Rated teen sex for strong innuendo.
V1.2-Pinkie Pie now enforcing RIAA guidelines.

Pinkie is a happy, smiling, bouncing, fourth wall breaking pony which everypony loves. Little do they know about the truth of Pinkie. Or the vital importance of her medication to prevent the crushing boredom. Short fic, only going to be two or three chapters long

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...

"We have to be brave now, Scootaloo," Dash said. "Just close your eyes, and it'll be all over by the time you open them again."

Hopes. Dreams. Aspirations. They're what everyone survives, and even thrives, on. What happens, then, when hopes and dreams are dashed? When something so monumentally destructive and life-changing occurs, and dreams, hopes, even ponies' lives are thrown into turmoil, where can solace be found? When somepony's entire world comes crumbling around them, who can they turn to for support? What can they do when everything they once had is shattered?

Hanna, the CEO of Hofvarpnir Studios, just won the contract to write the official My Little Pony MMO. Hanna has built an A.I. Princess Celestia and given her one basic drive: to satisfy everybody's values through friendship and ponies. Princess Celestia will satisfy your values through friendship and ponies, and it will be completely consensual.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page