Players control Snake through the game map and attempt to complete missions while avoiding being spotted by the enemy. The threat detection system is revamped, with the removal of the onscreen meter or gauge to indicate the player that they are in the 'alert/evasion/caution' state as in previous games, which have instead been replaced by visual and audio representations. Snake's binoculars have also been revamped; instead of selecting the binoculars as an item, the binoculars are hot keyed to a button.
The player is able to mark enemies and be aware of their locations in the iDroid's holographic display. There are directional cues to help players when an enemy sees them from a distance and gets closer to them. A new "Reflex Mode" is activated when an enemy finds Snake and the player only has a short window of time (in slow motion) to take out the enemy before he fully sounds the alarm (a hissing audio cue can be heard if the player is detected by searchlight).