Ok, so I want to put out the obvious obviousnessness from the Mosaic perspective, that is, to see Freespace 2's narrative as a retelling of the Exodus story. The hints to this connection are not even ovious, they are shouting from the rooftops that this is so, more ways than we can probably count, but still I'm feeling like doing that mathematics.
So, from this point of view, the story of FS2 begins within the Egyptian ideological hegemony. Khonsu the Second is the only species leader we are aware of, the leader that makes the Collossus unity speech, and he's an emperor. This hegemony is threatened by the secession of those humans who have a different "god", a different ideological viewpoint, one that does not see the Vasudan emperor as a credible reference. Bosch, the secessionist's messiah, starts a bloody civil war and opens up the connection with the true gods of the galaxy. A metaphysical battle ensues, successive waves of plagues are thrown into the Vasudan hegemony, but the GTVA goes on.
Notice that in the original Mosaic myth, the pharaoh admits defeat and let Moses and his people escape. In FS2 we do see Bosch escaping throughout GTVA systems with apparent concealed authorization from Command.
Bosch flees to the desert, wondering if he is taking his survivors to the promised land or to the valley of the kings. From the GTVA / Egyptian point of view, their army is undefeated, the biggest arsenal ever constructed. They will go, fight Moses and his God and they are very positive about it. What happens next is the fact that this new God is something the Egyptians never encountered before, a traumatic impossibility becomes very real, and their army is absolutely wiped out by a Sathanas Fleet / by the closing of the red sea. The survivors flee back to their empire, with a fear that will accompany them for the rest of their lives. Meanwhile, Moses gets to speak to God himself in mount Sinai, and, as I said before, this moral encounter with a vengeful, jealous god has a terrible consequence to all those who still dwell in the polytheistic ideologies of the past. Thus, the Iceni is a bloodshed and only the few who really believe get to the promised land.
But we don't get to see that, for we belong to the Egyptian army that has to flee back before being wiped out. We see the Mosaic events from the point of view of those who are not picked to be the Chosen People, and all we know about this God is that he is something Lacanianly terrible. Otherwordly and unintelligible. This is not your pharao's typical god. This is something else, this is a metaphysical revolution happening in our cosmos.
This is obviously the "canon" reading of FS2. Notice how every reference states clearly that the most important Chapter is precisely Exodus, and even admiral Petrarch mentions that the God of Moses is perhaps making an Exodus to their "home", their promised land.
So I just wanted to get this out of the way and now you can tell me how this has been said a thousand million times.