Periscope Up is a side-view horizontal-scrolling game where you control a submarine to save the world from an undersea nuclear base belonging to Britain in the year 2007. The 'Vax 3000' super-computer inside the base has malfunctioned and is ready to fire hundreds of missiles around the world and needs to be shut down. Problem is, all the entrances have been sealed as part of the battle procedure and the only way in is by underwater access tunnels used during construction. You must find the 8 digits to the pass-code to shutdown the computer as well as destroy six reactor pods.

As you you move around the tunnels you must open numbered gates by collecting the correct numbered keys but the keys are found in small areas. You can use a scoutcraft to move through the small gaps to collect the keys and dock back with the submarine. There are also electric gates that turn on and off, gates that open and shut and all walls of the tunnel must be avoided. Your submarine has three scoutcraft's and when they are lost then you lose one of three submarines and if you lose a submarine then any remaining scoutcraft is lost. Fuel and air are shown by decreasing gauges and if these run out then it is a loss of a submarine but more can be collected.