This story is a sequel to Rainbow Factory

Cloudsdale Weather Corporation has been running without incident for over twenty years. That is, until two foals manage to avoid being processed and find themselves in the haunted bowels of the massive facility. Can they make it out of the abandoned factory with their sanity intact? Will they uncover the secrets even a company as dark as the CWC is ashamed to keep? And what of the workers who help ensure that, in the end, not a single soul gets through...

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—[TVTropes Article]—[Plagen Shiki's Reading]—[The Song Inspired by the Story]—

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?

It seemed like it was going to be a perfect morning for Twilight, until she realized she had woken up with Rarity and Rainbow Dash, tenderly cuddling next to her on the bed. Just what the hay happened last night? And why do they keep calling Twilight 'mistress'?

Princess Luna's Lunar Stallions kidnap Twilight Sparkle when they see how lonely Luna is, and give her to the Princess as a gift. Nightmare Moon emerges from Princess Luna's psyche during the sleepover. The dark goddess would love nothing more than to have the beautiful mare all to herself, and the resulting chaos forces Celestia to call a psychologist to sort out Luna's multiple personalities.

There was only one explanation. For all of it. All of the strange, erratic behavior. Her irrational fear of the sun. Her nocturnal habits of locking herself in in the dark and closing all the blinds. Wearing her sunglasses everywhere, even inside! It was time to invest in some silver, garlic, and a wooden stake.

When a human is thrust into Equestria on a whim, he struggles to fit in with the locals of this strange land and tries to figure out how to get home, making new friends along the way.

Shining Armor and Cadence's spell reveals something completely unexpected as it expels Chrysalis and her changelings out of Canterlot: A secret kept from everypony for several years...

Now with a TV Tropes page! Warning: Will Contain spoilers.

Seriously, a lot.

(Now with a Spanish translation by the generous SPANIARD KIWI!)

Some things in this world happen by chance. Others do not. Twilight Sparkle is about to learn a disturbing truth that will turn her world upside down.

- Originally written May 2011 for Deviant Art

Reading this story first is strongly recommended:
(Blood is Thicker) http://ciroton.deviantart.com/gallery/26378692#/d3e1ndq

Credits:
~Image by JohnJoseco~ ~Edited by BrotherPrickle on Deviant Art~

"Like two peas in a pod we did everything together!" sang Twilight in the season finale. But what if she was letting on more than everyone else knew? What if Twilight really was a pea?