here's how I would handle the story after So3
1) nothing, at the ending it seems they evolved to what can be see the "artificial intelligence" they basically broke te 4th wall of their existance enabling them to live beyond their creator's will. Besides the only people that know there universe is a computer program is Fayt and the gang(I'm assumming that they told no one... and based on the endings no other people outside them seem to be aware and the crew seems to have not told anybody. Also there universe is still a UNIVERSE!!! and just based on the games beforehand there's alot left to explore, I find there existance no different than the "sub atomic universe theory" that we discuss today, let them live ther life exploring what in their universe
2) A mass exodus, since their universe was re-created at the ending boss battle, the gate that allowed them to transer from virtual to reality should still exist and since fayt's gang outide Sophia and Maria were also able to cross over as well. maybe this mean that basically eveyone from Fayt universe can cross over. maybe the can make a story about the migration to the "real" universe and the confilct that might ensue
2a) or if not everyone can cross over; along those lines fayt can continues his father's work to allow more people to transfer over
3) Focus on the real universe, we kow almost nothing of the real universe other than them creating this complex digital universe, it would be nice to focus on theie rise of their civilation which enable them to create this, maybe the reason from them creating a digital universe wasn't just for the hell of it, maybe something might be awry in the universe and they were looking forward to somehow digitalize their exsitance.
