Written with apologies to the late Arthur C. Clarke. Although, from what I've heard of him, he might just have been flattered...
The Tree of Harmony
Rainbow Dash dodged the black spell cast by The Pony of Shadows and chanced a look behind her at the Tree of Harmony. What she saw made her pause. "Everypony, look! The chest! It's opening up...!"
~*~*~Call it the Tree of Harmony.
For aeons, it has stood, awaiting the stimuli it required to begin the next phase of the mission. The return of the six harmony gems to its matrix marked that starting point but it was, by its nature, a device of the simplest responses. It was not capable of emotion so, when the six ponies with the activation artifacts for its next phase began to converge on its location, it felt neither anticpation or excitement. Nor would it have felt disappointment if they had passed it by and never returned. However, now that the activation artefacts had been revealed and attached as required, it was able to proceed with the tasks programmed into it by its creators using both science and magic so subtle as to be indistinguishable and unimaginable to even the wisest of the ponies of Equestria.
The beings that formed the Tree were not ponies, nor were they even remotely equinoid. However, they were flesh and blood. They were able to look out into the cosmos and feel awe, wonder and, ultimately, loneliness. Thus, as soon as their arts had advanced to the necessary level, they set out into the void to see if they truly were alone. Because, in all their voyages, they had found nothing more precious than Harmony, they chose to become its cultivators. They would sow, they would prune and nurture and sometimes, dispassionately, they would weed.
The exploration starship that arrived in what would one day, be called the Equis system had already been underway for tens of Equestrian years. In many ways this world was not that different from many others their people had discovered and identified in times past. When, during their careful survey of the world and its life-forms, they identified a possible vector from which the gift of Harmony could be bestowed on this world, they performed careful modifications on the starving, fading remaining population of a pony-like grazer-gatherer species living around what would one day be called the Dream Valley. Once the seeds of of survival, civilsation and progress were sown, the explorers removed their Rainbow Bridge and departed back into the void.
They knew that they would never come this way again but they would not have to. The magitech emissaries that they had left behind them would do the rest.
For thousands of years, civilsation waxed and wained across the face of Equestria, both for good and for ill. And throughout it all, the unchanging Everfree Forest guarded its secret. Then, finally, two desperate alicorns, facing the destruction of all that was good and harmonious in their world, uncovered its location, and the Tree responded precisely as its programs dictated.
The Creators of the Tree, meanwhile, had long since reached the absolute limits of their biology, no matter how great the medical, magical or mechanical augmentation. Thus, with remarkably little hesitation, they moved beyond the limits of their evolutionary past and transferred their essences into new, hardier and far more powerful forms. No longer would they fly in star-ships. They would be star ships.
However, the era of the machine-entities passed quickly. Soon, these remarkable beings realised that it was not flesh that was their limit but physical matter itself. So, they cast off their metal frames and ascended to a new plane of existance. On a thousand, thousand worlds and in the voids between them, their suddenly-soulless mechanical shells shuddered and writhed in a parody of life before falling still and began to decay.
Now, they were pure mind, will, memory and personality formed from magical fields sustained on a matrix of the very fundamental structure of the cosmos.
Although they were now almost without any limit, they were not gods; not yet, at least. The lessons of their long history had warned them against that conceit. Rather, although above almost all concerns of the physical, they still remembered their origins in the warm slime of a long-vanished sea...
And they still watched over the experiments that their ancestors had begun, so very, very long ago.
"Oh my sweet Celestia... It's full of rainbows...!"
Everypony knew that it was coming. Watchponys looked to the skies, great telescopes tracked aloft, defences were manned and every eye turned heavenward as history, as the ponies had known it, drew to a end...
Inspired by 2010 - A Pony Odyssey