I’m looking for the Nyx story where a group foalnaps her and uses a ritual to try and destroy her, but it fails. And also they set up a trap in that castle that rose from the ground in “Past Sins” that binds all the ponies, even the princesses while they do it.

And the reason it fails is because, unlike what they think, she is more than magical energy and in fact has a soul. And there was a part in it where Celestia showed this to Nyx by showing her the aura of her soul in a mirror.

The story you are looking for is "Nightmare Night and Nyx" by RealityCheck. He and his works are no longer on FimFiction, but you can find it here.

“Nightmare Night and Nyx,” along with the four other stories related to it, all written by RealityCheck, can be found at Archive of Our Own. As a side note, his username on that site is “RHJunior”.

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Aww. No wonder I couldn’t find it again. Wonder if it’s on FiMFetch. Why aren’t they here anymore?

YAY! It is on FiMFetch and available in epub too. Gonna download it now. Thanks guys. Really appreciate it.

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RC was getting flak (troubles) from lots of readers here, naturally a few had to ruin it for everyone so he left this site.

Sad but true... Loved his work.

Note that those versions are missing footnotes, I think... Better to use Fanfiction.net's versions, or WebArchive's?

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The one you’re looking for is nightmare night and Nyx However unfortunately it was removed from the site try googling the name you might be able to find it somewhere else but I know he moved at the authors name was reality check