Even if the ship's AI gained consciousness, why would it want to keep it so bad? Even if it was programmed to ensure its own survival, there is no reason for it to want to ensure it at the cost of other conscious lives.
I like the idea behind the gameplay and the setting, the frame of the game mechanics, but the plot would seriously need an explanation for the AI to decide to kill the very elements it was in fact programmed to protect. Why must machines be always either antagonists or saviors? XD
for that reason, I think some human should be convinced or corrupted or assimilated into cyborgs. That seems more plausible, and IMO more interesting than killing them all.