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Memetic eldritch horror
There’s two possibilities
1. The whole time they were just expirements and are being kept in a gigantic containment zone made to resemble ponyville, with the scientists watching from afar
2. Humans created the first ponies, possibly including the royal sisters, in an expirement in gene splicing, which worked better than they ever could have hoped. Then due to some self impnflicted disaster humanity was destroyed, leaving only the ponies behind. And after 1000s of years the last of the human ruins either decayed or where buried by time to never be found...until now
1. The whole time they were just expirements and are being kept in a gigantic containment zone made to resemble ponyville, with the scientists watching from afar
2. Humans created the first ponies, possibly including the royal sisters, in an expirement in gene splicing, which worked better than they ever could have hoped. Then due to some self i