Nightmare Moon: Twilight, why do you insist on fighting me? You could join me and we could rule together.
Twilight Sparkle: Never. You are a murder, a warlord, and a lair.
NMM: Did my sister tell you all that? SHE lied to you, Twilight. Did she even tell you about your mother?
TS: She died when you attacked Canterlot when I was a year old! You killed her.
NMM: You were snatched from your crib a month after your birth. I thought you were dead, I mourned for years, until I saw your picture in Celestia's orphanage. The title of your mother is the only thing this war has been about ever since that day, my sister can have anything she wants, but you.
TS: What should you care about me at all? Who am I to you?
NMM: Because, Twilight, I am your mother.
(yes I went that direction) Something I needed to get out of my head, and I would like to see something like this if any-one's read one.

2190260
How would that even work?
Did she steal a stallion's sperm and took it up with her to the moon and waited 982 years or so before using it then sending her kid down to the surface outside an orphanage?

That's, that's.... That's just terrible.
That's cheesier than Sheogorath's realm of madness.

2190301 I was thinking an alternative universe where she returned fifty years earlier or something. I had built a whole world in my head during work and didn't bother posting it. So an Alternate Universe.

2190260 I'd have to agree with MetaKnight145. Unless Nightmare Moon had somehow taken a stallion's sperm with her to the moon and waited about 982 years before using it, then sent Twilight down to the doorstep of an orphanage in Equestria, which would have been impossible to do due to being sealed in the moon, there is no way this idea would be even remotely possible.

And I don't think cryogenically freezing Twilight would work either, unless you really knew what you were doing.

2190377 Note to self, post Alternate Universe in such things.

I have read two stories like that where either Luna or Nightmare is Twilight's mother they are Child of the night and Daughter Of The Moon hope this helps

http://www.fimfiction.net/story/5523/nights-favoured-child

Nights Favored Child is a good one. She's only taken in as an adopted daughter, it's still really good!

I've read a few fics of conflict resulting from Nightmare Moon coming back early and having Twilight Sparkle as a filly before being sent back, but all dealing with the initial finding out and they are usually incomplete or not well written.

I would love to read a fic where the conflict is not about war and death, but the internal struggle of Twilight coming to grips with Moon being her mother, and how her friends try to help her cope after finding out.

I was going to suggest Night's Favored Child.