Alien 3 is a side-scrolling run and gun in which the player controls Ellen Ripley, the film's main character, who progresses through the Fiorina 161 prison colony that was featured in the film. The player can jump, shoot, climb ladders, crawl through tunnels, open doors, and use elevators. Unlike the film, Ripley has a large arsenal of weapons that can be used against the game's enemies, consisting of Aliens and Facehuggers.
Weapons include pulse rifles, flamethrowers, and grenades. A motion tracker warns the player of nearby enemies.
Level objectives are chosen from computer terminals, which are located throughout the game and also offer blueprints of the prison layout.
Objectives include sealing off doors to prevent Aliens from entering, and rescuing prisoners. A time limit is present on each level, and the player loses a life if the level is not completed before the time expires. The game concludes with a battle between Ripley and the Alien Queen