Area 51 is a first-person shooter, played from the perspective of the protagonist. (Code) , Ethan Cole. The game features operable machinery, including artillery turrets, besides the player's inventory of weapons.
Throughout the game, the player uses a variety of weapons, both human and alien in origin, to defeat their adversaries. Most weapons can only be wielded one handed, however the player can dual wield some weapons, such as the Shotgun and the Sub-Machine Gun. Each weapon can also be used as a melee weapon for close quarter combat. Each weapon has two modes of firing, the first being the primary method, while the second is of a much higher power level, at the cost of ammunition and accuracy to the player. The player can also use explosive grenades.
Midway through the game, Ethan Cole becomes infected with the mutagen, and the option to turn into a mutant temporarily is obtained. Mutating offers a variety of benefits, such as increased strength, stamina, as well as the initial ability to fire health-replenishing parasites as well as the later ability to contaminate enemies, both at the cost of mutation time reduction. While in a mutant form, players can easily spot enemies, which would otherwise be cloaked to the regular human eye, albeit with a slight ocular defect.
Players can replenish health and mutagen either through the use of medical syringes found throughout the game or by using parasites, and mutagen by melee combat or "using" infected corpses, or by finding mutagen syringes.
A notable aspect of gameplay is the ability to scan and analyze various objects in the game environment. This is possible by using the scanner present on the player's suit, worn throughout the game. While using a scanner, the player has no access to weapons, and must switch to an available weapon in order to fight (though they could still melee). Scanning provides detailed information on a player's surroundings, as well as combated enemies.