It had been a long hard struggle, but eventually, the Earth Ponies had won the war. And while they could grow their own food, they neglected to account for the fact that without the Pegasi to manage the weather, or the unicorns to cycle the day and night, they could not properly grow crops. Their harvests failed, the grass and forests withered and died. Soil dried to the point where even to break ground required a full day and a half of work.
Eventually, all that was left was a few scattered and decaying farms, and the bones of a failed country, shrouded in perpetual cold and night.
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Given their magical supremacy, it had been comparatively easy for the unicorns to win the war. They also had the presence of mind to keep the more talented and skilled members of the other races alive, and ruthlessly oppressed them, to ensure that nothing like that could ever happen again.
Within five generations, the small populace of Earth Ponies and Pegasi remaining were completely loyal. At least, until a strange creature crept into the capital of Unicornia one night, and laid ideas about rebellion into their heads.
“It is better to be free and dead,” it whispered to the Earth ponies and the Pegasi, “than alive and a slave.”
The cry reinvigorated the suppressed races, and they didn’t stop until they were all dead.
After that, infighting and chaos disintegrated the Court of Unicorns, and they soon lost the cohesion and numbers to keep raising and lowering the sun.
It only went downhill fast from there. Within a year, all that remained was a half-repaired city and the cackle of a mad god.
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It had only been with moderate ease that the pegasi won the war-they had the advantage of being the most militaristic of the three races, but lacked the magical advantage of the unicorns, or the sheer physical strength and tenacity of the earth ponies.
Unfortunately, their nature and aggression got the better of them. They took no prisoners, left nothing alive. They were a fearsome war machine, but lacked the ability to plan for the long term.
Within a year of their ‘victory’, they had all starved to death, only leaving behind a few scattered cloud cities, and in time, even these dispersed.