Players control Snake through the game map and attempt to complete missions while avoiding detection by the enemy. The threat detection system is revamped, with the removal of an on-screen 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to indicate the player that they are in the ‘alert/evasion/caution’ state as in previous games, which have instead been replaced by more subtle visual and audio cues. Snake’s binoculars have been revamped; instead of selecting the binoculars as an item, the binoculars are hotkeyed to a button. The player is able to mark enemies and monitor their locations in the holographic display of Snake’s iDroid. There are directional cues to help players when an enemy sees Snake from a distance and approaches him. A new “Reflex Mode” is triggered when an enemy finds Snake; the player only has a short window of time to take out the enemy before they fully sound the alarm. Lights can be shot out to further aid the player’s stealth efforts.

Ground Zeroes features seven missions in total, locked at individual levels. After completing the main mission, the player unlocks four subsequent missions in Camp Omega (referred to as “Side Ops”) set at different points in the day. These missions involve specific tasks, such as eliminating certain targets or obtaining classified information. After achieving a certain objective in the main mission, the player may unlock two additional “Extra Op” missions.