A century prior to the start of the game, the Kushan, humanoid inhabitants of the desert planet Kharak, discovered a spaceship buried in the sands, which holds a stone map marking Kharak and another planet across the galaxy labelled "Hiigara", meaning "home". The discovery united the clans of Kharak, who knew they were not indigenous to Kharak and craved to solve the mystery of how they came to this hostile planet. Together, they spent the next century developing and building a giant mothership that would carry 600,000 people to Hiigara, with neuroscientist Karan S'jet neurally wired into the ship as Fleet Command to replace an unsustainably large crew. The game opens with the maiden voyage of the mothership, testing the hyperspace drive which teleports the fleet to a new destination. Instead of the support ship that was expected to be there, the mothership finds a hostile alien fleet. After defeating them, the mothership returns to Kharak, to discover that the planet has been razed by another alien fleet, and that only the 600,000 migrants in suspended animation have survived. A captured enemy captain claims that the Kharak genocide was the consequence of their violation of a 4,000-year-old treaty between the interstellar Taiidan Empire and the Kushan, which forbids the latter from developing hyperspace technology.