Since the events in Star Control 2 the Ur-Quan have been pacified and the captain who bravely destroyed the Sa-Matra has had a horrible vision of the future. Suddenly without warning, all Hyperspace travel in the universe has stopped. Top scientists have pinpointed the cause of this disturbance somewhere in unexplored space in an area known as the Kessari Quadrant. Hastily assembling a fleet of ships as and an untested Precusor star drive... a loose alliance of alien races known as The League of Sentient Races sends a task force to the Kessari Quadrant. You are it's commander.

Star Control 3 features a new 3D star map, new alien races to discover, new worlds to explore and colonize, new artifacts to research and a new isometric Hyper Melee battle system for inter-starship battles.