Rarity's life was ruined by this, and she disappeared, leaving UNNAMED in the crystal empire hospital. She was raised in the orphanage until about the CMC's age, when she was kidnapped by Sombra and he taught her dark magic. By the time she was the mane six's age, she knew this was wrong and had fled to ponyville, where she discovered her connection to the elements of harmony.
As of the current timeline, Rarity is still missing and widely considered dead, while Sombra was killed in a war against the umbrums shortly after UNNAMED's escape. Almost the entire war was fought in the Frozen North, so there was little effect on Equestria. However; Cadence was assasinated by Umbrum and Radiant Hope took her place as Empress.