It was on my mind for a year, or around that. Now I decided to put my thoughts into words and see how it will work.
So, the thing is -- let's assume that the Season 6 will be the last one, and MLP Movie will conclude Friendship is Magic once and for all.
I'm describing my thoughts about this movie.
We've got the mane 6 ponies, who were summoned by Princess Celestia. As we've learned from season 4 finale, she can feel surges of magic on the distance. This is what happened.
She gives them a destination, and a map, where the source of such energy surges located. It's somewhere in the Unicorn Range mountains, between Canterlot and Vanhoover. And the ponies start their quest.
After some traveling, they arrive at the place, not knowing what to do, because the energy surges (Twilight can feel them now, too) come from the inside the mountain. Suddenly, Pinkie Pie, by accident, activates the mechanism, that reveals the thick door, leading inside. They carefully go there, watching their steps and looking around.
They discover the strange cave, filled with mist and containing one thing they didn't know how to describe -- a huge capsule, with a pony inside. She seems to be sleeping. The pony appears to be an earth type, but she doesn't have a cutie mark.
They wake her up. When she opens her eyes and sees the mane six, she reacts as if it was a dream. But they convince her, that she woke up.
The pony (let's name her Spring Breeze) tells them her story:
She belongs to the race, that lived in Equestria long before the current generation of ponies. Long before Discord's reign, long before Sombra, long before ponies even come to Equestria. (According to Heart's Warming Eve, ponies lived someplace else, before they came to Equestria, because Wendigos froze their home).
And that race (let's call them firstborns) achieved perfection in almost every sense and aspect. Their towns and cities were perfect. Their society was perfect. Their lives were perfect. They didn't know diseases, aging, depression, fear, sadness, hate, anger, disabilities, traumas. They didn't make mistakes. They didn't experience boredom.
Death was unknown for them. If they wanted, they could've just go to endless sleep to take the rest. Of course they could wake up in any time. They always behaved right, their trust was unbrakable, their loyalty was absolute, their care and friendliness were unmatched. They experienced no social and any other woes at all. They appeared as earth ponies, but each possesed approximely Celestia's level of power. They could fly without wings and cast powerful spells without horns. They also didn't have cutie marks, because they were so advanced, that they can define their favourite things to do without any marks, and were never mistaken. Only kids had marks, but at some point, they just disappeared, when a kid grows.
This perfection was the reason of their extinction. They were so eager to trust, that one evil soul outside of Equestria took advantage on them. They knew the golden rule, so they never abused each other' trust. Couldn't even think of it. But this soul actually decided to make the whole race die, so he could have all their powers, which would've made him tremendously powerful. So, he asked them to build a weapon of mass destruction, that would've destroyed their whole race.
The firstborns were always eager to help, so they immideately started to work. To prevent them from knowing the truth, the soul asked them not to pry. Since firstborns have no idea what does lie mean, they were happy to satisfy this request.
But there was one, who wasn't as perfect as they are. Spring Breeze was the flawed firstborn. She didn't think that somebody she's never seen wishes her people something good. She saw the device they were building and she was really suspicious about it. But she couldn't think that the soul will do something that bad. Until he actually launched that device.
Their whole civilization was wiped out withing a minute. But the soul didn't get what he wanted. Spring Breeze didn't sleep last night. She saw what was going on, but before she could warn the others, they were dead, because it caught them off-guard. She survived because she were able to make a shield that somehow protected her. She ran away to the mountains, and swiftly created a hiding spot. A capsule, that will make her safe during the sleep (as mentioned before, firstborn could go to sleep for any amount of time). She was afraid that he will come for her and destroy the last firstborn. She knew that until she's dead, the soul cannot have their combined might. But what Spring Breeze didn't know, is that the power of the firstborns will belong to her, since she's the last one alive.
But she realized that only after her awakening.
Ponies from mane 6 introduce her to Celestia, and she asks them to show Spring her new home. If only she knew what will happen after that...
Spring was destroyed. She saw what Equestria has become, saw that ponies were now consumed with anger, hatred and greed. That they are easy to betray each other, to take advantage on each other, to abuse each other. She saw that their socitey had so many woes, so many bad things that it hurted her beyond measure. Her home, Equestria, has become such a terrible place. Even if it was the second empire of ponies.
Filled with despair and sorrow, the last firstborn decided to make the terrbiel, but the only right decision -- she decided to cleanse the place. Destroy every single pony, every single living thing. Wipe out the life from the planet.
Celestia, of course, tried to resist. She brought the army of ponies, griffins, minotaurs, yaks, changelings, dragons against her, but what they could do? Nothing. Spring Breeze is too strong.
The mane six uses the Power of Friendship, the most powerful magic in the world against her, but guess what happens? It cannot harm her, because she bears so much goodness and pureness inside, that, instead of defeating her, Friendship empowers her, making Spring Breeze nigh-omnipotent, which gives her new hope. After destroying the world (Equestria Girls world included), she gives up her power and her life to create the third pony empire. Equestria, that she always dreamed about.
The perfect socitey, but without the firstborns' flaws. Smart, kind, caring and trustworthy civilization without woes of the previous generation. Ponies, who have no flaws, who can take care of themselves, who are able to stand against any threat, and deal with it without any effort. Civilization, that can reform any villain in no time. Just like the firstborns, they appeared as earth ponies, but had the power of the alicorn.
They last several minutes show the new life in the new Equestria. Show them, happy and safe, in their towns and cities, ready to celebrate Hearth's Warming Eve. Showing the world that is deprived from all bad things.