When Twilight is stolen from her home, fate intervenes and brings her straight to her destiny. After growing up sheltered and loved by the spirits of the Tree of Harmony, Twilight will grow into her place in Equestria like never before while she searches for the family that raised her and gets to know the one she's lost.

(Unapologetically OP Twilight, if you’re going to nitpick that point then you are welcome to leave at any time.)

"To the city of Titans you will go, to the days of future past and back through Apocalypse. See the end of ends, and then battle my illusion.

Twilight and friends find themselves in a world of heroes, changed into their power ponies selves. There they must ask, who sent them and why? Meanwhile, two young women deal with nightmares from their past, reminding them of the horrors that they have wrought. United, the trio must go through challenges and many battles to find the cause of all of it, and save the universe once again.

They will travel through hell and back, seeing once and for all the heart of a hero and why friendship will never fail.

A crossover between X-men, Teen Titans, and MLP.

In the timeline where the Changelings have taken over Equestria, Trixie has managed to find a shadow of her former life as an entertainer in Zecora's camp. She doesn't preform for giant crowds anymore, and while she misses the grandeur, she's managed to live a happy life entertaining the children of the camp with her stories and small tricks.
But all that comes crashing down when Queen Chrysalis and her Changelings attack. Now, Trixie must use every trick she has left to save her small fan club, and especially Ruby. Because Trixie made a promise to Berry Punch, and she won't allow herself to break that promise.

Written for EQD's Writer's Training Grounds

The Tears of Gaia. An artifact of unmeasurable magical power from the Ancient Days, when the Others ruled the land. If found, they would be the discovery of the century!
At least, those are Twilight Sparkle's thoughts. But something is stirring in lands to the south. Soon she will find that she and her friends are not the only ones who are after the legendary Tears. And so what starts as a simple research trip is soon to escalate into the greatest journey of the young ponies' lives, filled with new friends and foes, incredible danger and great adventure!

Accolades:
EqD featured- 21/09/2012
Now with its own TVTropes page right here!

NOTE: While I do appreciate all comments I get on this story, I would personally prefer if they could say a little more than the typical "Awesome chapter, I love it!" or whatever. What do you love about it? What struck you in this chapter? What would you like to see explored or expanded? Are there things you don't think are working and if so, how could they improve?? I have a pretty determined vision for this story, but it wouldn't hurt to know for the future!

Part 1 of the Shadow Trilogy

As Twilight Sparkle enters her third year amongst her friends in Ponyville, she finds herself plagued with strange dreams of an unknown power whispering dark secrets to her. The voices speak of Power, of the strength to protect what she holds most dear, of the great knowledge she could attain, such that no force could ever threaten her lands, or her friends, ever again.

Though she shrinks from this voice, the lure of greater knowledge, of magical power far beyond what she currently knows is enticing and alluring to her, eating away at her resolve even as the lack of rest begins to wear her physical defenses down.

What is this voice, and what does it plan for the most faithful student in Equestria?

Note: Events diverge from canon following the events of "Games Ponies Play"

Part 2 - The Twilight Fall
Part 3 - The Twilight War
Links removed in compliance with Fimfiction policies

Following the aftermath of Queen Chrysalis' evil plot to take over Equestria, and the transformation of the Changeling Kingdom, Princess Celestia has insisted that Twilight Sparkle be guarded 24/7 by a trained royal guard. Having refused the offer to be guarded before, Twilight is not too keen on being watched over every moment of every day.
Although she is doubtful at first, Twilight comes to believe that she and her friends have many challenges yet to face.
As this new development unfolds, a creature of unknown origins comes to Equestria with a dark purpose. Light becomes cast over the shadows of Equestria’s ancient past, and a well known truth may come to save this peaceful land.
Friendship is Magic.

A mysterious spell causes the mane six to slowly transform into monsters at night. Can they find a way to undo it before it becomes permanent?

A spell goes haywire, and Twilight and Rainbow Dash accidentally have their bodies switched.

***

An attempt to write an MLP episode.