As SilverFox said the additional missions start right after you finish the Vanilla campains, and thus you need not do anything but contiue on. These missions will take you to the other areas that are part of CF and you will meet Tougher NPCs. Changing the mod in anyway is not permited and thus all files should remain the same as you get them, plus it makes the mod even better to keep it as is. There are better guns and ships throughout the game as well shield up-grade and gens to help with your…