Growing up as a second class citizen on a back-water planet, Yuri dreamed of being able to travel the stars. After many years he saved up enough credits to buy transport off the planet, but space travel is forbidden to second class citizens, and he is chased by the security forces of the corrupt owner of the planet. To survive the dangers of space Yuri must become a captain, buy and customize star ships, and fight against hostile enemies both on the ground and in space.

The majority of Infinite Space's gameplay involves space ships, both in fighting and in modifying. All ships have a certain amount of space for extra modules to be added, and the abilities and shape of modules must be considered when choosing how to outfit a ship. In ship to ship combat you can control the distance your fleet is from the enemy fleet. During combat a command bar charges. You can use a small amount of the command bar to Dodge, use more to fire a Normal salvo, or expend almost all of it for a Barrage, which fires three times as many shots as Normal. If the opposing fleet uses Dodge before a Barrage then every shot will miss, leaving the attacking fleet at a disadvantage. If a Normal salvo is fired while the opposing fleet is Dodging, then every shot will hit and deal extra damage. Extra combat options come into play with larger star ships equipped with fighter hangars, special weapons, boarding parties, and officers with unique abilities.

The story progresses primarily with text dialogue and the occasional FMV. Sometimes the player is prompted to make a decision in dialogue for Yuri, and these decisions can have far reaching consequences. Additional officers can join Yuri through the story, by hiring them at a mercenary office, or by finding them on various planets. All officers have unique stats and abilities that make them better for a particular role, such as doctor, engineer, or pilot, than others, and these stats and abilities increase in level from combat.