After the changelings' failed invasion of Canterlot, Twilight tries to soothe some of Ponyville's rampant paranoia by casting a spell to prove there are no imposters hiding in the town. But her spell leaves her in an alien body, facing a mob of angry ponies who just don't believe her when she says she is Twilight Sparkle.

Or, at least, she was Twilight Sparkle, anyway...

Featured on Equestria Daily, 2/17/13
Cover art is by the awesome and amazing Conicer

My name is Aideen; I know, I know, it's a stupid name for a pony, and if you pronounce it wrongly it even sounds male, but let's not get sidetracked here. I've lived through multiple mental breakdowns and severe physical beatings, but who hasn't in the dear wastelands? I can, however, claim that I'm a unique nutcase; there's something that differentiates me from the regular nutcases out there: The same evil entity that transformed Princess Luna into Nightmare Moon once upon a time wants me to be her new host.
Uhm... fun stuff...

Rated teen for gore

original story by the one and only Kkat

This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

Equestria is a land of magic and harmony, a peaceful realm ruled by immortal and benevolent monarchs. At what cost is this possible?

Following the discovery of a strange and powerful device, Twilight Sparkle is whisked away to the edges of a land she thought she knew so well. Here, surrounded by ponies whose very existences have been kept secret, she must contend with vicious enemies, hostile allies, and the truth.

Chapters 1-16 edited by KiltedKey

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

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

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page