I think what was originally planned was for them to go and start populating a new planet after they began searching for Lost Jerusalem at the end of the game (much like they began populating the xenogears planet in that game).
And then the rest of the series probably would have taken place on that planet that they showed at the very end of Ep. III.
So I think xenosaga would have ended up in much the same way that xenogears did with Shion being referenced to in much the same way that the first Elly and Miang were referenced to. |