Rouge's early history was most likely largely the same as her Mobius Prime counterpart's. The point of divergence was when Knuckles became corrupted by his chaos powers and decided to conquer Mobius. Eventually, Rouge joined the countless heroes and villains alike that fell to Knuckles, now having assumed the mantle of Enerjak, and had her Core removed.
After the loss of her Core, Rouge's body was hung on the inner walls of Enerjak's Citadel like a trophy. During Enerjak’s final battle against Silver the Hedgehog, Rouge's Prelate was summoned among a horde in order to overwhelm the young time-traveler, but to no avail.