Problem... when the Pegasus disappeared, it had no fighters. All fighters and non-essential personnel were evacuated to Galactica. Therfore, even it its possible to code, your entire career as a player aboard the Pegasus, would consist of being a turret gunner. Perhaps, the Pegasus will encounter the remains of another Battlestar, with some intact fighters and additional components intact. Pilots would be drafted from the remaining crew and the primary plot would be trying to locate the trail of the Galactican fleet, while evaiding Cylons and avoid them following you to the Galactica.
How's that?