Question: What should I do in Deep Six mission if the scientist will not unlock the airlock?  During the Deep Six mission where I am supposed to free the scientist to operate the airlock, the game never moves forward.

Answer: After freeing the scientist, he runs to a green computer console next to an elevator and then stops. I can't get him into the elevator, I can't get him to come back down to the airlock level.

Try going back two previous saved game and going to this section again. The game should randomize and work correctly from this point. If you are playing the game in "New York Minute" mode, you might be running out of time which would keep you from finishing the level.