As in the original Metal Gear, the player's objective is to infiltrate the enemy's stronghold while avoiding detection from enemy soldiers or surveillance devices. To fulfill their mission, the player must collect a variety of weapons and equipment, such as firearms, explosives, and rations, as well as card keys to access new areas. If the player is discovered by the enemy, the game will go into an alert phase, causing enemy soldiers to enter the screen and attack the player. The player must defeat a certain number of enemy soldiers to return to the infiltration phase or go to a different floor or area. In some cases, particularly when a guard sees the player and only a single exclamation mark (!) appears over his head instead of two (!!), the player can also escape the alert phase by simply moving to the adjacent screen.
A change to the original Metal Gear formula is the fact that the player now begins the game with a combat knife and a handgun already in their equipment. The A button is used for firearms and explosives as in the original game, whereas the B button is used for a melee attack with a punch or a knife depending on which one is assigned. The knife can be used to instantly kill guards at close range, but guards who are defeated with punches instead will occasionally leave behind an ammo box or a single ration unit.
As in the original Metal Gear, Snake's maximum health and carrying capacity are determined by his rank, with the highest level being six stars. The player must rescue various hostages scattered throughout various areas until enough have been rescued for a promotion. The player will also encounter enemy officers in certain rooms who can be interrogated by applying truth gas unto them. Successful interrogations are counted alongside rescued hostages for promotions.
The interface of the player's transceiver has also been greatly changed from the original Metal Gear. Instead of dialing frequency numbers, Snake now has a set list of three contacts (John, Nick, and Jennifer) that he can communicate with and a radar that is activated whenever it detects a tracking signal transmitting from a nearby area. Unlike in the original Metal Gear, the transceiver cannot be used when the player enters alert mode.
Snake's Revenge features a varied progression of areas such as a jungle, a warehouse, a cargo ship, and a train, as well as the usual encounters with enemy bosses. In addition to the standard top-view areas, the player must also go through a series of side-view areas that play in a manner similar to Rush 'n Attack, in which Snake proceeds by walking, jumping, or crawling on his stomach while avoiding detection as usual. While in a side-view area, the player is limited to only the knife or handgun as their standard weapon, although plastic explosives can be planted as well to eliminate obstructions. Some of these areas require the player to crawl underwater to progress, resulting in the need for oxygen tanks to proceed without sustaining damage. Each time Snake's oxygen gauge runs out, a tank will be used automatically to refill the gauge until supplies last.
