The real question isn't what happens to the Pegasus, that's pretty obvious. The real questions are:
1. What happens to Corporeal Number Six?
2. What's the giant ship?
Theories on both:
1. Lives, maybe? Baltar kinda fixes her, except then she goes all BERSERKER, and since she's already killed 7 people, she's probably pretty damned dangerous. (The real question is, how'd they find out she was a Cylon?) But, which goes back to the idea of Cylon factions, if she's from the "Let's kill humanity! They suck!" faction, do they keep her as a prisoner or do they kill her?
2. Remember the farms from Caprica? Bingo. Farm, so they can monitor Boomer's progress, and should it prove to be successful, they start cloning ASAP. Maybe a colony ship for Earth? Base stars seemed to be the Cylon equivalent of battlestars, so I don't know why they'd have a ship larger than that. Raider factory doesn't make much sense; the jump distance is large enough that they SHOULDN'T have to have one that close.
Survivors of Caprica, maybe?
