Ok I had this idea bouncing in my head forever (and this random dialog popped into my head while I've been stuck inside due to weather), anyway I in no way think I can do this justice, i just want some opinions and if this is in the wrong place please let me know as the forums and groups on this site are confusing to me...

Time wise this snippet would take place before the history shown in Hearth's Warming Eve.

“The Kingdom has fallen. The effects of the last spell have spread farther and faster than we thought, those who weren’t affected are being rounded up for execution.”

“What of the young ones.”

“Hit as well, only the celestial ones, escaped unscathed”

“The others?”

“They were victims of the spell, we have them hidden, but soon the three factions will be looking for them, there are so few of us left.”

“We must protect them, given time I may be able to reverse it.”

“We don’t have time Starswirl, I don’t have much longer, and with my death, Harmony’s children will have no protection.”

“What about the Crystal Princess?”

“She was hit as well, the king has perished in the war, the Princess was brought here for safekeeping, she was hit trying to protect the younger ones.”

“What should I do my queen?”

“The celestial ones will be here, the guards have them, once they get here I need you to cast a spell to take them to where they will be safe.”

“Your Highness, the spell was never tested, they, they could be lost forever.”

“If the factions get them Harmony will never return, and the children will be lost forever to us anyway. We have to give them the chance. Now we must go, We need to get them to safety.”

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It's in the right place. This is The Idea Bronies. It's the Writer's Group you can't post story ideas in.

And that sounds interesting. Do you have a summary?

Basically years (lots and lots of years) before Hearths Warming Eve Alicorns were the only type of Pony. Then a plague (or a spell) over took them one by one, changing them into the three tribes, their magic limited to earth, air, and matter manipulation, and lifespan cut. Those who were changed began to rebel, either by killing the alicorns (so they could not be reborn), or infecting them. The three tribes found any infected and brought them into their tribes. The Queen saw what was happening and managed (with Starswirl's help) to rescue the remaining parts of the Royal Family. Those being the Celestial ones (Luna, Celestia, and Their sister), and six other fillies (this may change to 9...). To protect them the Queen and Starswirl start looking for a spell to protect them. Unfortunately the six others were hit by the spell (curse/plague whatever) causing them to change and the tribes to want to get to them. In a last ditch effort they get the children together and Luna and Celestia add their power, knowing that using the spell would cause harm to their younger sister in her state also allow her to be changed by starswirl to be like the others. The spell sent the 7 young ones through time to be reborn, and Celestia and Luna to be trapped in their respective domains until Harmony could once again reign. Unfortunately during the spell the tribes broke in, infecting starswirl and killing the queen, disrupting the spell long enough for their destination to not be known.
The three tribes take over, create their own societies and live their lives, Starswirl being the only one who truly knows what happened to the children (having fooled them into thinking he was helping to destroy the last of the alicorns) passed along his knowledge to his apprentice Clover and passed away, leading to the events shown in Hearths Warming Eve.
After Hearths warming eve, the world was still in Chaos, Discord took over the newly united equestria and was well on his way to breaking the truce that had formed, if not for Clover spreading the word about the Celestial Ones, In an attempt to make the tale come true He went on a journey to where Starswirl had said long ago the Queen of all had lived and found the Tree of Harmony standing where the Queen had died. Focusing his magic he asked the tree for help, and the tree answered him.
Celestia and Luna freed from their respective domains now took on the fight against discord, only winning by going to the tree of Harmony and getting the elements from it. Once defeated the united tribes listened to the now elderly Clover (who along with the other assistants convinced the rulers) to let the two take on their birthright as Princesses of Equestria (the two not wanting the title of queen).
Around the same time Luna and Celestia see that the Crystal Empire (once ruled by the Alicorn King) has now fallen to darkness by King Sombra, who had found an ancient attempt at a cure and had managed semi alicorn powers, or possibly he *was* the alicorn king, but I'm not sure yet), They defeat Sombra causing the Crystal Empire to dissappear much to the two's horror as they had hoped one of the children would be discovered there)
Nightmare Moon Happens, years pass
Celestia now saddened by the loss of her sister finds the first child, Cadence, as she's now called living as a pegasus with earth pony parents, Cadence becomes an alicorn (must read that book again...)
Celestia thought she'd never find the others, until a little purple unicorn took the entrance exam for her school...

..ok a bit longer than a summary, but...