I actually thought of that myself, but I have no idea how to make mods, so I threw the idea out.
However, in my version, you would fly for the Ancients. I had some cool ideas for Ancient ships (the Minotaur - class destroyer would look so cool if someone actually made a model of it). In the first mission, you were patrolling near the newly - activated Knossos device (the third one, that is present in Into the Lion's den), and then the Ancients have their first encounter with the Shivans, they are chased back into another system, which the Shivans eventually supernova, creating the Gamma Draconis nebula, and they keep pushing forward, until eventually you stage a last - ditch defense mission at the Ancient's home planet, but get defeated, and the very last mission is where most of the Ancient fleet has been destroyed, and you just have a few wings of fighters and bombers left, and you chase the Lucifer - class destroyer through subspace after it wiped out your home planet, and if you win you disable it so it drifts in subspace. Possibly a precursor to Derelict, if the makers of that would allow it.