In a gloomy not-so-distant future, mankind have finally made it to Mars. The colonization of the red planet is vital for humanity's survival, as the heavily polluted Earth's resources are nearly depleted. At the same time, the Taar, a mysterious alien race that lost their homeworld many centuries ago, has decided to take Mars as their new home.

As the war between the two species erupts, the player has to choose his side and lead his people to ultimate domination over the red planet. Things become even more complicated when the ruins of an extinct ancient civilization are found on Mars, revealing immensely destructive weapons that could easily turn the tide of the war in favor of the faction that manages to gain control over them first.

Dark Colony is a real-time strategy with heavy emphasis on the actual combat. Resource gathering, base construction and unit production have been made as simple and fast as possible, allowing the player to focus on decimating the enemy armies. Ancient artifacts, available in some of the missions, provide unique options for beating the odds, even when they seem to be against you (and they often will).

The game plot advances through short cutscenes, briefings and debriefings which detail the development of the war. The game also offers various promotions and decorations that you can earn for your player character, who will actually be present on the battlefield, acting as a more powerful and durable trooper with some special abilities (such as calling in reinforcements and inspiring the regular troopers).