During gameplay, the player navigates through several missions based on stages from Metal Gear Solid 4, each introduced by brief text summarizing the story so far. The player moves their finger across the screen to aim, tapping to fire, and moving their fingers together or apart to zoom in or out with a sniper rifle, removing their fingers from the screen to get behind cover and avoid enemy fire. The main character's primary weapons, an assault rifle and a sniper rifle, can be rotated with one another by pinching the device's screen. Gako and Kerotan statues can be shot to gain health and weaponry such as rocket launchers.
The main objective of most missions is to kill a set number of enemies. Enemies include hostile PMC soldiers, Haven Troopers and Gekkos. There are also friendly targets which the player is penalised for shooting at. Some sections contain 'Boss fights', where the player fights a boss from the Metal Gear Solid 4 storyline; e.g. Laughing Octopus.
At the end of each mission, the player is awarded a rank based on their performance, similar to other Metal Gear Solid games. Higher ranks award more Drebin Points, which can be used to buy rewards such as iPhone character wallpapers.
The updated "complete" version (2.0.0) of MGST was released on April 22, 2009. This update adds eight more levels and covers the story from the arrival to Shadow Moses Island to the final showdown with Liquid Ocelot. Among the eight levels, four are boss battles (e.g. Metal Gear RAY, Screaming Mantis).
Version 2.1.0, released on May 3, 2009, added 15 new wallpapers, many of which cannot be previewed until certain objectives are met.