Mighty's early history was most likely largely the same as his Mobius Prime counterpart's. The point of divergence was when Knuckles became corrupted by his chaos powers and decided to conquer Mobius. As Knuckles' madness grew, Mighty and the Chaotix would openly turn against him. Eventually, Mighty joined the countless heroes and villains alike that fell to Knuckles, now having assumed the mantle of Enerjak, and had his Core removed.
Over the years, Mighty's Prelate, Prelate-M, was summoned by Enerjak on a number of occasions for his campaigns, right up until Enerjak's defeat.