First, the setting is the same Mars that you saw in the original game. Many of the same organizations and individuals will be showing up again. What's different is that 39 Dark is a look at the colony from the people up instead of from the government down. Some number of years have passed since Kelly Perkins attempted to fix the colony's problems. Things have not gone well. Now a protest movement, 39 Dark, has gained a lot of traction. No one can ignore them any longer. You'll be playing as Lane Novak, the leader of 39 Dark, as he or she tries to take matters into her own hands.
In terms of mechanics, the core system from Mars Colony is still there. However, a few things are different and a few things are new. One of the biggest additions to the game, and something I'm very excited about, are the action levels. In 39 Dark, a Progress Scene now takes place at one of three action levels: Civil Protest, Civil Disobedience, and Violent Uprising. Depending on the action level, you might be more effective, but you might also have to pay a higher price for failure. Because the system is still push-your-luck, you never quite know how things will turn out -- and that lends a definite edge of tension to the game.
There are other differences, especially including the sequel rules, which allow you to tie a game of Mars Colony directly to a game of 39 Dark.
Overall, if you enjoyed Mars Colony, I think you'll love 39 Dark. There is plenty of new material to keep you interested, and to add nuance to your previous Mars Colony stories.