The Fergana was flying from Point A to Point B. They were sabotaged and rerouted to go to System C, which was a known black zone for ships (FTL didn't work there), and it crashed. The survivors became the founders of the Dome. The original intent was to pack up and leave in a few generations, once they'd managed to fix the ship and figure out how to leave the black zone. This task became less urgent with every generation, and then The Upheaval happened and the ship was essentially buried, and thus forgotten entirely.