I suppose an excellent question would be if the Shadow helping Eggman was a fake...where was the real Shadow that whole time? He wasn't in virtual reality for THAT long I would think.
Yeah, Shadow got out of the Virtual reality before Eggman's forces surged into the city. The prologue tried to trick prople into thinking that the Shadow working for Eggman IS the Shadow in the prologue, so it didn't tell us where the real Shadow went.
Why does Eggman need a Metal Sonic clone? Why can the Zavok clone talk if he has no soul? How did Omega get fixed at the end?