After the Changeling invasion, Celestia and Luna make the decision to have Twilight investigate the Elements of Harmony and solve the mystery of their power.

A thousand years later, Rainbow Dash awakens in a world she does not recognize. She has no idea how or why she came to be there. She does not know the language, the geography or any of the rules of this new time. She soon finds allies in Star Fall, a scholarly pegasus whose Talent is Magic, and Astrid, Star Fall's Griffin guardian. Together they set out to discover why Dash has been sent to the future, and how she might return to when she belongs.

War threatens the nations, a Nightmare stalks the shadows, and Rainbow Dash's arrival has turned her into a wild card in a deadly game that pits the law on both sides of a broken Equestria against a mysterious criminal figure, Max Cash. Yet the stakes are higher than anyone knows, for in her research Twilight Sparkle discovered a dark secret about the Elements, something that will shake the foundations of the world.

Cover image by SierraEx
Has a TvTropes page

In the middle of the night, Princess Cadence and her husband are woken by the news that a Changeling drone has been captured. The creature is alone and unaggressive, showing no wish to attack or change shape. Its fate is decided without much difficulty--as an obvious reject of the Swarm and a threat to Cadence's people, it must be destroyed.
But this is no ordinary drone. It can speak, and appears to be separate from the hive mind of the Swarm. It claims to have been sent as an ambassador--Chrysalis, queen of the Changelings, wants to forge an alliance with Cadence's kingdom.
But why now? Why send this strangely intelligent drone? And how will Cadence's people react to learning that their rulers are harboring a Changeling?

WARNING: Contains an OC, much headcanon speculation, and possibly violence/gore further in.

(Image courtesy of the talented Hero, my good friend and artist.)

Twilight Sparkle, Arcane Mage, knows that there is some truth to the story of Nightmare Moon, but her mentor, Princess Celestia, dismisses the matter in a heartbeat. She sends Twilight to the town of Magiville to oversee preparations for the Summer Sun Celebration, much to Twilight's distaste.
Unbeknownst to her, the darkness is gathering in Mystica. Assassins lurk in the shadows, Undead gather in the forest, werewolves sharpen their claws, and criminals and mercenaries prepare themselves.
To win the coming battle, Twilight will have to rely on her wits, her magic, and the five mages she's been saddled with. No matter how much they annoy her.
Rated teen for violence and language. Humanized, action-y. Based on the first two episodes, with some large changes made.

Twilight and her friends enjoy a relaxing day at the beach, when Rainbow Dash has a startling encounter that leads to an exciting undersea adventure.

Featured on Equestria Daily on 09/28/2012

At first glance, Princess Luna's charioteers might appear to be little more than Royal Guards dressed in festive apparel for Nightmare Night. However, there is far more to the story than that - the Night Guards once played a pivotal role in the history of Equestria, and have sacrificed more for their beloved princess than most ponies are even aware of.

Shortly after a party that went terribly wrong, Rainbow Dash begins acting in ways nopony ever expected! Now it's up to both a current and an old friend of Dash's to make sense of things... before Rainbow Dash has no friends left!

(Cover art by... Jowybean? Hey, I'm just as surprised as you!)