On the surface, Space Trouble looks like an orthodox shooter, but it has an unorthodox twist: Don't shoot! You navigate your ship through an asteroid field, with a finite fuel supply. From time to time, enemy ships come into view and try to hunt you down. Shoot them down, but bear in mind that each shot costs a little bit of fuel. Sometimes, you will encounter a fuel supply, and strewn throughout the game are powerups which boost your "flight record", which is turned to score as you complete a level. As the game progresses, the asteroids change into other obstacles, such as flying saucers, mines and organic blobs which take several shots to kill. Each enemy ship also has its own movement patterns, some hunting you down, some avoiding your shots, and some just bumbling straight forward.
When you've passed four different fields, you encounter a mother ship. Docking with the ship requires minute precision, or you will crash and die. The ship teleports you to the next level, which is much like the first.