Deus Ex takes place from a first-person perspective. It was designed to incorporate gameplay elements from four types of games: role-playing, first-person shooter, adventure and "immersive simulation", the latter being defined as a game in which "nothing reminds you that you're just playing a game". The player assumes the role of JC Denton, a "nanotech"-augmented operative of United Nations Anti-Terrorist Coalition (UNATCO). This nanotechnology is a central gameplay mechanism, and allows players to perform superhuman feats.
As the player accomplishes objectives, the player character is rewarded with "skill points". Skill points are used to enhance a character's abilities in eleven different areas, and were designed to provide players with a way to customize their characters; a player might create a combat-focused character by increasing proficiency with pistols or rifles, while a stealthy character can be created by focusing on lock picking and computer hacking abilities. There are four different levels of proficiency in each skill, with the skill point cost increasing for each successive level.
Weapons may be customized through "weapon modifications", which can be found or purchased throughout the game. The player might add scopes, silencers, or laser sights; increase the weapon's range, accuracy, or magazine size; or decrease its recoil and reload time. Not all modifications are available to all weapons; for example, a rocket launcher cannot be silenced, and recoil cannot be reduced on a flamethrower.
Players are further encouraged to customize their characters through nano-augmentations — cybernetic devices that grant characters superhuman powers. While the game contains eighteen different nano-augmentations, the player can install a maximum of nine, as each must be used on a certain part of the body: one in the arms, legs, eyes, and head; two underneath the skin; and three in the torso. This forces the player to choose carefully between the benefits offered by each augmentation. For example, the arm augmentation requires the player to decide between boosting their character's skill hand-to-hand combat or his ability to lift heavy objects.
Interaction with non-player characters was a large design focus. When the player interacts with a non-player character, the game will enter a cutscene-like conversation mode where the player advances the conversation by selecting from a list of dialogue options. The player's choices often have a substantial effect on both gameplay and plot, as non-player characters will react in different ways depending on the selected answer (e.g. rudeness makes them less likely to provide assistance).
Deus Ex features combat similar to first-person shooters, with real-time action, a first-person perspective and reflex-based gameplay. As the player will often encounter enemies in groups, combat often tends toward a tactical approach, including the use of cover, strafing, and "hit-and-run". A USA Today reviewer found "At the easiest difficulty setting, your character is pureed again and again by an onslaught of human and robotic terrorists until you learn the value of stealth." However, through the game's role-playing systems (see below) it is possible to develop a character's skills and augmentations to create a tank-like combat specialist with the ability to deal and absorb large amounts of damage. Non-player characters will praise or criticize the main character depending on his use of force, incorporating a moral element into the gameplay.
Deus Ex features a heads-up display crosshair, whose size dynamically shows where shots will fall based on movement, aim and the weapon in use; the reticle expands while the player is moving or shifting his or her aim, and slowly shrinks to its original size while no actions are taken. How quickly the reticle shrinks depends on the character's proficiency with the equipped weapon, the number of accuracy modifications added to the weapon, and the level of the "targeting" nano-augmentation.
Deus Ex features twenty-four weapons, ranging from crowbars, electroshock weapons and riot baton, to laser guided anti-tank rockets and assault rifles; both lethal and non-lethal weapons are available. The player can also make use of several weapons of opportunity, such as fire extinguishers.
Gameplay in Deus Ex emphasizes player choice, which GameSpot's review explains: "Deus Ex is quite long for an action-packed first-person game", it states, "but even so, most of its situations present you with two or three possible solutions." Objectives can be completed in numerous ways, including stealth, sniping, heavy frontal assault, dialogue, or engineering and computer hacking. This level of freedom requires that levels, characters, and puzzles be designed with significant redundancy, as a single play-through of the game will miss large sections of dialogue, areas, and other content.
Because of its design focus on player choice, Deus Ex has been compared with System Shock, a game that inspired its design. Together, these factors give the game a great degree of replayability, as the player will have vastly different experiences depending on which methods he or she uses to accomplish objectives.
Deus Ex was designed as a single player game, and the initial releases of the Windows and Macintosh versions of the game did not include multiplayer functionality. Support for multiplayer modes was later incorporated through patches. The component includes three game modes: deathmatch, basic team deathmatch, and advanced team deathmatch. Only five maps, based on levels from the single-player portion of the game, were included with the original multiplayer patch, but many user-created maps now exist. The PlayStation 2 release of Deus Ex does not offer a multiplayer mode.