Returning to the formula of dual joystick shooting paired with environmental puzzle solving, PJS2 is a direct follow-up to the first game, and the story is no exception. Picking up where the original PixelJunk Shooter left off, players must navigate their ship through the innards of the monster that has just swallowed them whole. In this story mode, the game supports co-op for two players, where the second player can drop in or drop out at any time between levels. As in the first game, elements of the environment, especially water, can be used to offset some of the hazards that enemies and other environmental characteristics, such as lava, pose to the player. However, the sequel brings more to the table in terms of enemy variety right off the bat, and expands on this environmental idea with many new types of hazards, even adding a light and dark mechanic in later chapters. This broadening of gameplay ideas creates more challenge and a wider array of puzzles than the first game focused on.
The game has a few episodes, and within each episode are a 5 stages. and every stage contains between 3 and 6 levels. In each level the goal is to rescue all the survivors on the map, and because sometimes things don't go as planned you can at maximum kill 5 of the survivors. There are also special survivors and they have a flag, and a name, and when you have rescued them there will be some story advancement. In the game you will use a lot of fluids like lava and water. And you use these fluids to solve puzzle's and advance in the level. the fluids will move like fluids and will interact als fluids. So if lava and water collide. the lava will be solidficated and the water will go up into thin air. You also have weapons. an ordinary pie-shooter and rockets. If you use rockets or get to close to hot fluids your ship will heat up. and then you need to fly into the water to cool off.
The player moves the ship with the left stick, orients the ship with the right stick, fires with R1/R2, grapples with L1/L2, and spins by spinning the right stick. In addition to puzzle solving, there are several types of enemies in each section that should be destroyed. Destroyed enemies dispense coins. Some of their fire can be deflected with a spin or destroyed by your fire or a fluid. You must also collect treasure hidden throughout the stages, as they are used to unlock further stages. There is also a shield power-up that may be collected, which prevents overheating by proximity or brief contact, though that destroys the shield.
Collecting 100 coins or finding a 1-up will remove a survivor death.
For the first time in the series, this game features online play on the PS3. In the Online Battle mode, players are alternately tasked with attacking and defending an area containing survivors. Completing various objectives earns the player Q-bucks, which can be spent to unlock and upgrade weapons and abilities. These range from purely offensive items like larger missiles, to defensive items or those that will obfuscate the other player's controls or interface.
The game was released for PlayStation Network on March 1, 2011, for $9.99.