At first, pony society tried to accept them. Love and tolerance and such; most ponies saw no reason why these strange in-betweens could not live among them. Even before the ponification program was put into effect, few truly believed that powerful magic like the Conversion Bureau's could be without risks or side-effects. The unfortunate cases of the in-betweeners only confirmed these suspicions. Many of them were stricken with sorrow at their condition; still others found that their minds were at constant war with themselves, waging an endless war of human vs. pony sensibilities.
The day of the in-betweeners' revolt will forever be known as the Night of Terror. The streets ran with blood as they lashed out with impossibly, horrifyingly coordinated malice. Homes burned. Innocent villagers were murdered in their sleep. Mayoral offices, guard outposts, and mail routes fell to the rioters in a matter of hours. The only thing that saved pony society from meeting a bloody end at the hands of the in-betweeners was the relatively small number of rioters who dared to continue the fight when faced with the power of the first alicorn, Queen Reverie, nee Christina Dawn. The changelings who remained converged on the town where she had taken residence, thinking to decapitate pony society in a climactic battle--and every last member of the attacking army broke itself against the Queen's godlike power.
Queen Reverie, with her once-human failings, decreed that the in-betweeners be banished to the Outlands for all time, subject to immediate imprisonment if ever seen near a pony settlement.
Reverie would never see another in-betweener in her lifetime, nor would Queen Nocturne after her, nor Queen Daybreak, or Queen Astra. Improbably, the in-betweeners seemed to be willing to abide by the terms of their exile.
In truth, of course, the in-betweeners were among them, unseen. For thousands of years, dozens of generations, they watched. They watched as the old world's dreams of peace and love came to full fruition, dreams that no longer included them. They watched science crumble without humans to tend it, and they watched its slow resurgence. They watched nations rot away to make way for one glorious, beautiful, harmonious Equestria.
Each one of them is born with their mother whispering to them what they are: An aberration, an exile, a hated enemy of ponykind. The name given to them in the beginning still remains: In-betweeners. In-between what? The infants invariably ask their parents, and the answer is always "Between hope and despair." The in-betweeners do not know what they are, nor do they remember what they once were or why the first ones were exiled. They have only stories, stories that teach them hate, sorrow, jealousy... and hunger.
It was inevitable that they would one day lash out again. Like the first time, so many thousands of years ago, their target was the home village of the Queen, though this time there was no queen but a Princess, and she lived in the glorious city of Canterlot.
Princess Celestia's niece was to be married. All of ponykind's eyes would be on Canterlot. There, the in-betweeners would rise again.