While all this is happening, a group of genetically engineered former slaves, the Neosapians, are secretely planning a rebellion. Neosapians, who were once used as slave miners in the harsh conditions of Mars, are physically very strong and very smart. They rebelled 50 years before, but that rebellion was crushed. The new insurrection is planned by the Governor of Mars, Phaeton.
Once the Exofleet is dispatched, the launch the rebellion and capture the homeworlds in short order.
The two seasons that the show was on the air followed the progress of the war, as seen through the eyes of Able Squad. Able squad is a group of elite soldiers - J.T. Marsh, Nara Burns, Maggie Weston, Kaz Takagi, Alec Deleon, Rita Torres, Wolf Bronski, and Marsala (a Neosapian).
The second season ends with the defeat of the Neosapians and the liberation of the homeworlds. However, the second season ended with a cliff-hanger, and the show was cancelled soon-after. Many speculate that the third season and afterward would have been about a war against extra-solar aliens, and that the humans and neosapians would be forced to ally with each other.