WMG / Ancient-Shivan War

The player character is the female Ancient from the original FreeSpace.

It would make sense as the Ancient in the cutscenes does sound like she didn't just experience the end but rather fought to try and prevent it. Also every now and again when you kill and enemy in the game, one of your wingmen would say "An honourable kill, sister." implying that the player character is female. This wouldn't be the first time a mod has tried to exploit a fan theory.