When Twilight Sparkle and her friends used the Elements (again) on Nightmare Moon, it had a different effect than when Celestia had used them. Rather than banishing Luna once more to the moon, it ripped the Nightmare out of her and restored her to her uncorrupted self.
The Elements had grown stronger over the years. Previously, they could not cure Luna, so the only option was either to kill her or imprison her and hope for a solution at a later date. This is why Celestia set the banishment for a thousand years. Fortunately, as fate would have it, six ponies happened to come along whose virtues matched the Elements precisely, at just the right time to get the job done.
The Elements had been held in close proximity to the Tree of Harmony for about 1200 years. They were once connected to the tree directly, but at some point after the castle was built, thieves were nearly able to make off with them. The sisters had decided to keep them hidden in the castle instead, and Everfree only very slowly degenerated into the creepy forest of modern times. Most of that transformation happened after the battle with Nightmare Moon when the castle was abandoned.
Three years after the return of Luna, the Everfree Forest suddenly began spreading aggressively and grew much more dangerous. It turned out that the removal of the Elements by Twilight and her friends had caused the Tree of Harmony to become seriously weakened.
The elements needed to be returned to the tree directly in order to restore Everfree to being relatively safe to travel through. The bearers fought their way to the heart of the forest and discovered the Tree of Harmony at a small inset of a deep ravine, very close to the old castle.
After this, life in Equestria moved on as normal, and the citizens were relatively happy. Mortal ponies remained entirely unaware of the long and troubling history behind Everfree, or the true nature of alicorns. Celestia and Luna continued to rule, and the six Element bearers served the nation in various ways according to their virtues for several years until the Great War with the zebras changed everything once more.
But what happened to the Nightmare? The unborn foal, forcibly taken and corrupted by Hyperion all those millennia ago, still existed. It was only a matter of time before she would find a way to return. The only remaining question was whether she would still be compelled by Hyperion’s directive or if she finally, after all this time, had volition of her own.
So we're going PAST the present day? That was unexpected. I've been checking in on this story occasionally, and I had expected it to end about the time the show started, with the elements curing Luna being treated as a good ending point. Now I have no idea where the story is going to go or where it's going to end, and it's kind of exciting.
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The chronicle has an epilogue I'll be publishing shortly with an Author's Note at the end.
So while you were originally correct about it only giving history up to the point of the mane-six, this is only the beginning of a much, much greater journey.
Too bad that didn't happen the first time, would have make things far easier.
In wonder why though?
The foal herself? Or rather her descendants?
I mean it had been quite a while, way longer than the most pony's natural lifespan.
I feel like this point will be addressed later.
(Or had it already been addressed somewhere else?)
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That's MLP's issue. Why did the Elements do something different the first time they were used on NMM than they did the 2nd time? Who knows? But in my story, the Nightmare was defeated by war spells and left for dead but actually survived, hid away in exile for a long while and then came back to finish what she started.
She's an immortal alicorn, so...
All of this was meant to lead into Past Sins.