When Trixie used a teleportation spell, she hoped to disappear away from Ponyville, but not go so far as to go to an alternate timeline. And in this alternative timeline, Nightmare Moon rules Equestria. As if that weren't the worst, Nightmare Moon ends up liking Trixie and wants her to stay in the castle to keep her company. Now, Trixie needs to find a way to return home. But will she really want to go back to the original Equestria, especially after being humiliated by Twilight?

Nightmare Moon returns to Equestria after her thousand year banishment. But is it the right Equestria?

The violence is minor, as is the language.

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Love is one feeling that can never be taken from someone's heart. No matter how many years of separation, no matter what wrongs were done in the past, no matter how much enmity exists between two ponies, love will always stand; at least that's what Nightmare Moon is hoping for. 700 years ago was the last time she had seen her sister Celestia, and her departing words had simply been 'I love you'. Now, after so long, Nightmare Moon's heart longs for its other half; and thus, she has brought Celestia back from the far away, magically void lands she cast her to so long ago. Now, she wonders if her sister will ever find it in her heart to forgive her for what she's done, and if their lives together can ever resume as they once had.

Takes place 300 years before when Luna would have returned from her banishment to the moon, and takes place in a universe where Nightmare Moon was never banished in the first place.

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SPOILERS IN THE COMMENTS

The Elements of Harmony aren’t weapons. This is a basic fact, they are an extension of the Tree of Harmony a being that thinks for itself. A weapon is a mindless tool of destruction, there is no Harmony in destruction. A thousand years ago the two Royal Sisters fought. Nightmare Moon was a problem the Tree, nor Celestia saw coming. So at that moment when Celestia used the elements the tree guided the power to act the only way it could think of at that moment. Give the Tree of Harmony time to come up with a solution. A plan was formed and the Elements rested to build up the magic needed to save Luna, and Nightmare Moon. A thousand years later the time came to set the plan in motion...

Nightmare Moon captures Celestia. Celestia is kind of annoyed.

Spoilers, look at the tags.

Nightmare Moon has been banished to the moon for a thousand years. However, while she may be imprisoned, she’s not entirely powerless. Bodily, she is grounded. But her essence can still wander, and she’s found that the dreamscape is a wonderful place to occupy her time.

On a dark night filled with even darker magics, an insane cult attempts to give Nightmare Moon a body and life of her own, utterly separate from Princess Luna. But, when the spell is interrupted by Celestia, something unexpected is created.

Now, a little black alicorn filly named Nyx finds herself living under the care of Twilight Sparkle, only to be haunted by memories and emotions from her past. Is she Nightmare Moon reborn or is she simply a doppelganger with a soul and mind of her own? Can Twilight Sparkle protect Nyx from those who refuse to see past her dragon eyes and black coat?

Or, will Nyx be forced to inherit the sins that may not even be hers and become the greatest evil Equestria has ever known?

Welcome to the Lunar Republic and the reign of Nightmare Moon. In Ponyville, the survivors of those first tumultuous years after the fall of Endless Night struggle just to feed the few who are left. In Canterlot a young stallion dreams of standing with honour before the First Citizen herself, while in the far north, an ancient evil dreams of southern conquests.

Chapter one of this story was the winning entry of the Hazardous Writing Materials and Challenges group's April 2016 competition.
Edited by RadicalDishonesty, artwork by the amazing WingFlyte (click here for DeviantArt page.)

On the longest day, of the thousandth year, the stars aided in her escape.

Then Nightmare Moon looked out upon the land that would soon be her empire, and found a world she no longer existed in. In a thousand years, she had been all but forgotten.
She could conquer, and continue to be hated. She could put aside her pride, and be redundant. Or, she could disappear, and fade into the glorious night.

AN: While Princess of Equestria takes place before this, neither are required reading for the other. Rather, they complement each other.

When Trixie's father tells the story of Nightmare Moon, Trixie feels pity and sorrow, and she wants to find a way to go to the moon, so that the mare on the moon has a company.