The game is set on a fictional Mars colony - the so-called "Dark Colony" - in the year 2137. Humans have discovered a "remarkable energy source" by the name of Petra-7 on the red planet. Figuring they'd rather not choke on the atmosphere of Mars whilst mining this precious stuff, the Humans begin terraforming the planet and by the time the game starts the project has produced jungles and deserts habitable by people. All seems to be going well, until the Taar show up. The Taar are aliens (the ones from the Roswell incident no less) from a scattered and dying race looking for a new homeworld, and Mars seems to fit the bill. Before they can move in though, they have to get rid of those pesky Humans.
The game consists of two campaigns where you can either play as the Humans, commanding a colonization force from Pan Luma Industries (one of the Earth corporations along with Aerogen and Stratus who are in charge of the Mars project) whose goal is to defend against and defeat the alien threat, or as the Grays, where you have to defeat the Human presence on Mars and claim it for your own.
Source: Wikipedia, "Dark Colony," available under the CC-BY-SA License.