The basics of Star Control - two ships, competing in a one-on-one battle - takes quite a nod from the arcade game Space Wars, but then ends up having its own identity with its extra features.

The basics of the game involves two ships at battle with each other, which are usually from opposing sides: one ship from the Ur-Quan Hierarchy, the other from the Alliance of Free Stars (or even two ships from the same side can do battle against each other during Practice mode). Each ship has their own characteristics, strengths and weaknesses as they are pitted against each other in battle.

Each ship has a certain amount of fuel and crew manifest that will contribute (or detract) to a battle. Ships also burn fuel during a melee, but not in the traditional sense: thrusting will not burn up fuel, but firing a weapon and/or using a ship's special power will. Using too much fuel will render a ship incapable of attacking their opponent for up to several seconds at a time.

Each time a ship takes damage during battle, one or more of its crew members will die. Once the final crew member of a ship dies, the ship then self-destructs and the opposing ship is declared the winner; if both ships destroy each other, then the event is considered a tie if a full game is being played and those were the last ships from each opposing fleet (see Full games section).

When each battle begins, most of the time (with the exception of when a VUX Intruder is involved) both ships start out on opposite ends of the screen, being off in the distance. Once they get closer they will get bigger and the players will have less time to react to each other and/or other obstacles in the playfield, such as a planet that is in each sector (which colliding with a planet will cost the player at least one member of its crew) or the occasional asteroid that flies by, which can impede a player's attack. An asteroid can be destroyed by either player's fire.

Onscreen displays shows fuel and crew amounts as well as a representation of alien or human entities that are working the craft; i. e., on the Earthling cruiser, when a player turns their ship, the onscreen pilot will react, and when the primary weapon is fired, the other onscreen person will press a button.