Earth is hungry, cold, and cramped; its peoples need food, energy, and new frontiers. The Pleidans (called the Grays by Earthlings, and familiar to anyone hanging around Roswell 50 years ago), a race which apparently specializes in genetic manipulation, have troubles of their own; genetic experimentation gone awry apparently decimated their culture, and they're struggling to rebound. That was the main (and largely forgettable) premise from the original Dark Colony.
Council Wars, which requires the original Dark Colony to be installed, adds 16 additional missions that once again pits Grays against Earthlings in canned missions. There’s also the regular stuff you’d expect to find in an expansion pack, such as adding new units, new buildings or environments. Novel environments include an alien fortress or Area 51. Also new is a third neutral species that you can capture and use to your own nefarious goals.