hmm, refresh my memory, that's the one where the Sovereign first shows up, right? Did download a modified soveriegn by any chance? If the game can't find everything it needs it does that, and most modded sovs don't work in SP, mainly because they replace the quantum torpedoes with a quantum pulse turret, or they are missing the plasma torpedoes, go into the hardpoint and add them back into the hardpoint, that should fix it. If that didn't work download the Supermod 3.