well, seeing as how the blight terraformed new Tera, eventually it will run out of material to break down, and it would effectively starve to death
perhaps as the star ship is fueling on the gas giant they could come by this information (the sky dock was also a com relay), and thus would choose to go back to New Tera rather then risk another trip to the stars
New Tera would have a new atmosphere, but it still would not be breathable by humans, why? because of the intense volcanic activity would spew tons of C02 and sulfur compounds into the atmosphere, making it toxic, so from a game play stand point they would still have tubes and sealed buildings, and war would still be fought by robots