From what I gathered, NDS plans to keep the story the same, but flesh out some of the details and the world with the help of Chris Avellone.
This might be way to go – keep the plot simple and straightforward, but add a lot of local (environmental) story-telling of the events:
If you want atmosphere in a game, things have to look real, and they also have to feel real. So in addition to the 3-D physical environment, we have a plot that goes beyond “bad things have happened, go and kill everyone.” There are mystery elements, as you go through the space station and unravel what actually happened. There are log messages and email messages from the past and the present that you read during the game, and we’ve tried to make them more than “you must pull lever N” and instead make them feel as though they came from and are going to someone real.
On one level, for instance, you’ll read log messages from members of the human resistance to each other about how they’re going to try to break through the blast door and attempt to reach the next level. And then as you approach the blast door, you start encountering all these bodies, and just in front of the door there’s this ring of corpses. So you say “Wow, this is where the last resistance got wiped out… what’s on the other side of this door?” And then you open the door and there’s a group of deadly warbots. When you’re done, on one side of the door there’s a ring of human bodies, but on the other side there’s a pile of broken robots, where you’ve just taken out the forces that destroyed the last humans on the colony. And not every player will notice that, but the ones that do will get an immense kick out of it. So we have that kind of atmosphere and context to the things you do in the game.