In PixelJunk Shooter, up to two players can control their own subterranean vehicles to rescue a number of surviving scientists trapped underground. Using their ships' missiles, players can defeat enemies and destroy weak rock to progress through the environment. In addition to rock and ice, players must manipulate three types of fluid (water, magma, and ferrofluid) in order to reach the survivors. Once each survivor is rescued or killed, players may progress to the next part of the stage. If too many survivors are killed, players are forced to quit or restart the stage. The game has fifteen stages divided evenly among three "episodes", each episode ending with a boss encounter.