(all information taken from wikipedia )

The Kushan people lived on a planet called Kharak, a desert world so hot and inhospitable that only the polar regions were settled. They are a tribal society, organized primarily into independent sociopolitical entities called kiithid (singular: kiith), each of which embodies unique religious and cultural traits. For the great majority of Kharak's past, there was war between at least two kiithid at a time. The major kiith include Gaalsien, Naabal, Paktu, Sobaan, S'jet, and Manaan.

Kharak's extremely inhospitable climate eventually led many Kushan to question how they evolved on it in the first place, and DNA comparisons between Kushans and other native life eventually proved that, in fact, they hadn't. The question of where they did come from was answered by a malfunctioning satellite which accidentally scanned the surface of the planet, penetrating to a depth of 75 meters, and detected metal in the vast, inhospitable reaches of the equatorial deserts. An expedition sent to the site discovered a huge alien ship, the Khar-Toba (First City). Within the Khar-Toba was found an artifact that would change Kushan life forever: an artificially-created stone, etched with a crude galactic map. A dot on a spiral arm clearly represented Kharak; a line connected this dot to another on the inner rim, a dot labeled with a word so ancient that it predated the kiithid themselves:

All but the most radical kiithid eventually united toward the goal of journeying towards the game's eponymous homeworld and discovering the reasons behind their departure. However, this was far easier said than done. No one on Kharak could decide just what the journey would entail, so the decision was made to construct a ship that could handle anything. The resulting vessel, known only as The Mothership, is over 30 kilometers on its longest axis and required 60 years to build. It demanded huge advances in science and technology (many of them back-engineered from the Khar-Toba) and every resource Kharak could muster. 600,000 colonists were frozen in cryogenic sleep for the journey, and an internal construction bay and hangar allowed for rapid construction and storage of all fleet auxiliaries. The bridge crew was staffed day and night by the best tacticians, navigators, diplomats and scientists Kharak had to offer. As no computers could be developed that were powerful or efficient enough to coordinate all this activity, Karan S'jet, a young female neuroscientist, integrated her physical body into the Mothership to serve as its living CPU. She now serves as Fleet Command.

Spoiler warning: Plot and/or ending details follow.

After an initial tutorial mission, the Mothership tests her hyperdrive by jumping to the outskirts of the Kharak system. An assistant ship, the Khar-Selim, has been on its way to the same coordinates for the last ten years, but when the Mothership arrives, only wreckage greets them. The ship has been destroyed by unidentified hostile forces (eventually identified as the Turanic Raiders), which attack the Mothership as well. After defending herself, the Mothership returns to Kharak for repairs. However, in the Mothership's absence, Kharak was attacked by the Taiidan, a large interstellar empire which now controls Hiigara and viciously opposes the Kushan attempt to reclaim their homeworld. The remaining surface population of Kharak, several million in number, is annihilated by atmosphere deprivation weapons. The Kushan race, now reduced to 650,000 people (the vast majority of which are frozen aboard the cryotrays), swears revenge and sets off after the Taiidani fleet.

During their travels, the Kushan survivors meet the Bentusi, a benevolent group of traders who provide technology and information. They also re-experience the Turanic Raiders, and encounter the enigmatic Kadeshi, who defend their chosen nebula home with fanatical zeal. All the while the Kushan continue to research new technologies and spacecraft advances, eventually amassing a significant fleet, and face increasing hostility from the Taiidan Empire.

After the Mothership and the Kushan rescue a Bentusi tradeship from Taiidan forces, the Bentusi reveal their history: the Kushan once ruled a mighty empire from Hiigara, but were overthrown by the Taiidan. The Hiigarans were exiled to Kharak (a small segment stayed in a nebula, eventually becoming the Kadeshi) and were forbidden on pain of death from entering hyperspace again (resulting in the horrific, if technically lawful, razing of Kharak). The Taiidan Emperor, claim the Bentusi, will stop at nothing to prevent the Exiles from reaching their goal. However, the Kushan have allies in the form of the Bentusi (Homeworld 2 reveals that they assisted the Taiidan in unseating the Hiigarans, fearing Hiigaran pride, but the Taiidan have become just as bad) and a groundswell of rebellion within the Taiidani Empire itself, most specifically in the form of military defector Captain Elson, who provides needed intelligence and a supplemental fleet.

In a final battle above Hiigara, the Kushan fleet, augmented by Captain Elson's forces, destroys the Taiidan Emperor and succeeds in reclaiming their Homeworld.