PixelJunk Shooter 2 is the sequel to PixelJunk Shooter. It is set immediately after the events of the first game where the player controls a space ship to investigate a distress signal from the mining colony Apoxus Prime. After defeating the final oil drill boss, a large monster appears from below the surface and swallows the space ship. The first level in this game then starts inside the monster's stomach. Just like the first game the main goal is to save all survivors and collect as many gems as possible along the way. For a certain amount of gems collected a new level is opened up. A typical environment consists of a small area where the ship can be moved in any direction with the screen scrolling both vertically and horizontally. The ship can shoot enemies in any direction and a secondary function is used to grab a survivor with an extension from the ship when nearby. The grab function is also used to collect gems. When all survivors are rescued, a gate is opened and the ship can proceed to the next area until the entire level is completed. Rescuing all survivors is not required; when one dies because of the player's ship's weapon, enemies or environmental hazards, the gate still opens when there are no more survivors alive. Levels can be replayed to improve the score. The ship has a basic shooting option and by holding it homing rockets are activated. These however fill up a meter with four bars in the bottom left corner. When full, the ship explodes and the level needs to be restarted. The fourth 'danger' bar is also reached right away when the ship comes in contact with a dangerous substance or is shot. By moving away from danger, or by going into water or ice, the ship can be cooled down, depleting the meter. Many elements from the first game return, such as the focus on physics and the way substances react, for instance forming stone when magma and water are combined. The ship is still vulnerable to certain influences and needs to be cooled down regularly. Other gameplay elements and substances from the first game also return. This game introduces a purple substance inside the monster similar to the gas of the previous game and a green substance that can only be removed with water. There is also constant movement to the environment as it is organic. Also new is the ability to use the grab function to latch unto fixed points and launch the ship through a quick rotation. A new type of enemy can only be taken out by grabbing it out of its holder and then shooting it. Similar to the first game the ship can equip suits at fixed locations with new abilities. The hungry suit for instance allows you to eat away through parts of the monster's insides to create a passage and the light suit shoots bolts of light. The game consists of three episodes, split up in different levels with multiple areas for each and three bosses in total. After the episode inside the monster, the second episode combines most of the environments and substances from the first game with some new elements. The last episode introduces darkness as a new gameplay element. Many parts of the scenery are blacked out with only vague green outlines, making it more difficult to spot enemies. Light sources can be picked and carried around to find your way around. Others are fixed in the environment, but can be grabbed or shot to make them swing. After completing the three episodes and collecting all treasure, an extra level is opened up with different gameplay. It is played as a horizontally scrolling shoot 'em up where the screen moves at a fixed speed. The player dodges obstacles and shoots. This level also incorporates some substances from the main game. Just like the original game cooperative local multiplayer is available for the single-player campaign. The competitive online multiplayer is new. It is played one-on-one through four rounds where players take turns rescuing and defending scientists, also while shooting each other. By progressing different types of weapons can be unlocked, such as tsunamis, reflective shots and gravity shifts.

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