Well, I did a run where I didn't destroy the basestar (I had to specifically order the other fighters not to approach it), and as I suspected, nothing happened until about eight minutes in, the other two basestars jumped in and Theseus fled, leaving behind Obit (which seemed to be an acceptable outcome to continue the game, despite not destroying the first baseship). I'm wondering if disabling the communications would stop the other two baseships from coming in (probably not, because not having the time-pressure to leave would mean Obit wouldn't get left and Mission 3 wouldn't happen). I'm wondering if the FTLs might come into play (say, there's a timer after the Baseship falls below a certain health percentage, and if it isn't destroyed before it runs out, it jumps), but the ship never ran in my test.
(If we were looking for alternate mission outcomes, are there any particular tips for what to try? I might've been spoiled by the Xantos-style
mission plotting of the BTRL demo. So far, I flew over to one of the distant baseships in Mission 4, but all it did was sit there. I did enjoy the failure in Mission 3, though I was hoping for the Theseus
to turn hostile and try shooting me down when the Centurions got to Aux Fire Control. That's actually something I liked about the game in general, the opportunity to see all the Cylons' crazy plans actually work, like the boarding action or the Olympic Carrier, which totally got me the first time).