Actually, another idea: The final boss is going to be Alpha. Your choice of whatever shenanigans bring this about:
Omega decides to see where the strength of your party comes from(whether it's because of Alpha himself lending you battle power inside the sim, or your character).
Alpha is ultimately part of Omega, and he recalls/absorbs/fuses for the fight.
You beat Omega, but this simply means that Alpha is now the strongest component of the 'Scape and immediately takes Omega's place as the master/tester.
*Insert reason that sounds plausible here.*
Then imagine Chocobo (Savage) times 1000.
