"I'm telling you, they control everything"
"Will you stop with that"
"How else do you explain it?? All these mares together in one place, the magic of friendship, Twilight becoming a Princess ... It's all planned! It's all a secret organisation!"
"Orrrr it's Princess Celestia knowing lots of things and having lots of advisors. Besides, we had Starswirl and the Pillars, it's not a new thing"
"I think it's moonbats"
"Shut up, Bookmark. I've seen the hints they leave, their signature"
"What kind of secret organisation would leave clues? That makes no sense!"
"So w e know they are around and they watch us!!"
"Moonbats ..."
"Shut up, Bookmark"
"That's dumb, you're dumb, I'm going back to play Oubliettes and Ogres with Lucky Dice"
"You said he was busy!"
"He just doesn't want you playing; you keep saying the game is rigged!"
"IT IS!"
"Can I be a moonbat?"
"SHUT UP BOOKMARK!"

Everyone has heard some version of the same story; a secret organisation of some sort wishes to exert power over the Powers-That-Be, and rule in the shadows, or cause some sort of discourse in order to ensure no one undesirable group has complete control. More often than not, such talk is nothing more than paranoid fantastic thinking, or else takes a very small, very niche group and exaggerates their wants, power and influence.
It shouldn't exist in Equestria; after all, the power structure is very clear. Two Princess, one who rules the sun and one who rules the moon. They look after Equestria together, barring a small incident when one banished the other for turning a little evil. Two more Princesses ascended, one for the frozen Crystal Empire, and the other for the concept of Friendship. What use is a secret group in this setting?

Except, for once, there was some truth in it. But the truth was more sad than it was shocking.

The IlLUNAnati were a small, niche group that was founded on the day the Royal Sisters took their place as rulers over the three tribes of Equestria. Always made up of three members, so votes would not be hung, they always comprised of one Earth pony, one Pegasus pony, and one Unicorn pony. Gender varied; sometimes two mares one stallion, sometimes two stallions, one mare. Never three stallions, never three mares. Their duty, as they saw it, was to watch over the lunar royal and protect her. As she grew into her position, their group became complacent, neglecting their basic duties as they foresaw themselves becoming obsolete.
The rise of Nightmare Moon shattered them. Realising they had utterly failed their Princess, they disbanded, and vanished into deeper obscurity.

One year before the return of Nightmare Moon, three ponies independently rediscovered the tale of Princess Luna. Whisper Blue, the Earth pony Royal Archivist. Crystal Clear, the Unicorn junior assistant at the Equestria National Observatory. Silver Song, the Pegasus opera understudy. Each had their own tale of how they found the history of the lost Royal Sister. Each came together to meet, to find the ILUNAnati's ruined cause and hidden influence, and they pledged to retake the sacred duty to watch over the younger Princess.

Some say they had a hoof in the events that turned Nightmare Moon back into Princess Luna.

That is up for the world, should they know, to decide.

With Equestria calm and the Princesses ruling side-by-side again, things had fallen into a state of tranquil patience, ready and waiting to step in should Luna become threatened.
And while Equestria's Princess Luna was safe, the same couldn't be said for another, in a world far different to the one governed by the magic of friendship ...

"I've heard the cry again ..."

Crystal Clear looked up from her book, peering over her glasses at Whisper Blue. The Earth mare was sitting by the large pool in the middle of the ILUNAnati's secret layer in the forgotten and secret bowls of Canterlot Castle. The pool was filled with moonwater, a traditional place of meditation and future seeing, and sometimes healing for members of the organisation. Even with her hood up and most of her face obscured by shadow, Crystal Clear could see the concern on Whisper Blue's face.
"What kind of cries?"

"Fear. Pain. Despair" Whisper Blue shivered, "It must be from Our Princess. There's no other voice that would be so clear"

"I checked; Princess Luna is safe" Silver Song confirmed, coming down the stairs from one of the many secret entrances to the lair, "She is having some midnight tea and a snack before going dreamwalking; the guards are all alert, Princess Celestia is deep in sleep. I hear nothing from Ponyville or the Crystal Empire. If it's from Princess Luna, it's not from-"

"This place" Whisper Blue looked up, her ears forward as she tried to hear the sound better, "It cannot be from this place. It must be from another world"

"Another ... world?" Crystal Clear closed her book softly, "Which world? Is it in the Canterlot High world? The last crisis was solved by Sunset Shimmer, the Princess should be safe there too"

Whisper Blue shook her head, "I hear distress from mirrors if it is from that place. This ... This cry is darker, more horrible ..."

"... " Without a word, Silver Song and Crystal Clear joined Whisper Blue at the moonwaters, all three looking at the surface of the dark, gently rippling pool. A silvery film covered the surface, a testament of the subtle, velvety magic that infused it, and allowed them to see past this world and into others with the right concentration. Each pony dipped their left hoof into the water, adding the magic of their tribe, willing the sound to be clearer, more precise.

All three winced as the cry echoed around their minds.

"NO! No, no please! I WON'T SUBMIT! I AM THE PRINCESS OF EQUESTRIA! I WILL NEVER BOW TO YOU!"

"Princess ..." Crystal Clear whispered, just as another, rougher voice spoke.

"You will bow down as your sister did, I will make you red whatever it takes"
"I REFUSE! YOU CANNOT DO THIS!"
"Look at what I did to your wings, your horn. You want this, it is your place. Your land, your throne, your cunt, they're all mine"

Silver Song almost recoiled from the language, his mouth agape in horror.

The following sounds they heard were almost too terrible to describe. Cries, screams, the sound of flesh being unwillingly taken. Tears poured down the face of all three ILUNAnati members, as Whisper Blue wrenched her hoof violently out of the water, shaking, breaking their connection.

"Princess ... " Crystal clear started to sob, covering her eyes with her hoof.

"I didn't hear that, I did not just hear that" Silver Song shook his head, trying to forget the awful sounds, knowing what he had just heard but trying his hardest to stop it becoming a memory, to stop it becoming ingrained in his mind.

"We must go to this place" Whisper Blue stated, her teeth gritted, "We must rescue Our Princess from this terrible fate"

"We must"

"We must"

Drying their eyes, they stood before the moonwaters, taking a deep breath.

As a trio, they slipped into the waters, their shoulders pressed side-by-side. Crystal Clear's horn, Silver Song's wings, Whisper Blue's hooves, all glowed with their tribal magic, as they sank into the shallow waters, suddenly deep and endless, and decended down to find the world that held their tortured Princess ...

Author's Note

Whisper Blue, Crystal Clear and Silver Song are all my OCs and hopefully I will expand on them better through this story. They are left mostly obscure as they are hooded in this chapter and I just wanted to establish a bit of an opening scene.

Here goes!!