Star Control II is a game based on exploration, space combat, diplomacy and resource gathering. Your main starship is the Precursor vessel and it can be used to travel between star systems; this uses up fuel. Raw materials are used as currency to make purchases in your space station headquarters; you can buy fuel, as well as improve your starship, buy smaller ships to accompany the starship as a fleet (to fight enemies), and hire crewmembers (who represent the "health" of your ships).

Raw materials are found on surfaces of planets and moons throughout the galaxy; you have to send a landing module to the planet and then guide it around the surface as it picks up the materials you found earlier with your scanner. Each planet is unique in the type of minerals and metals it is formed of. Some planets are plagued by natural dangers such as lightning storms, earthquakes or lava which can damage or destroy your landing modules. Non-sentient lifeforms can also be found and stunned to obtain biological samples. Special installations, objects and ruins can also be found on certain planets and explored.