Some time during the 2050's, the world is a dangerous place as terrorists, drug czars, and outlaw states rule, using violence and subterfuge as tools in their push for global conquest. A deadly virus dubbed "gray death" is running rampant throughout the world and the only known cure is a chemical known as "Ambrosia" manufactured by the VersaLife corporation. However Ambrosia supplies are scarce and world governments, particularly the United States, carefully monitor and control who receives this cure. As protest against these events, French terrorist organization "Silhouette" bombs the historic symbol of friendship between French and American people, The Statue of Liberty. In response to this attack, the United Nations Anti-Terrorist Coalition (UNATCO) organization is formed. Building a headquarters underground at Liberty Island, its mission is to attack terrorism and maintain peace around the world. JC Denton is a nano-enhanced agent who has been primed for UNATCO service. While JC's brother Paul is already an active agent, JC is beginning his first day of service when the National Secessionist Forces (NSF) suddenly raid a supply of Ambrosia at UNATCO headquarters.

Deus Ex is a dark cyberpunk game that combines gameplay styles of first-person shooter and RPG, with elements of stealth and puzzle-solving. The player assumes the role of JC Denton, UNATCO anti-terrorist agent. Pitted against an elaborate global conspiracy, he must interact with characters, pick up weapons and complete objectives. While JC is essentially fixed within the mission-framework of the game, he can be customized in areas such as weapons, technical skills and physical prowess. Completing objectives rewards the player with skill points, which may be distributed to increase JC's proficiencies in eleven different disciplines. The player can choose to increase the damage JC inflicts with various types of weapons, improve his lock-picking or computer hacking abilities, etc. Each such discipline has four levels of proficiency.

Another way of customizing JC is applying nano-augmentations to his body. These cybernetic implants bestow the hero with super-human abilities, and can be installed on different body parts, up to nine at the same time. Along with combat-related benefits, nano-augmentations also grant JC abilities that can be used to overcome certain obstacles within the game world. Examples of those are jumping to extreme heights, swimming, lifting heavy objects, etc. Weapons can be customized as well: their range, accuracy, and magazine sizes can be increased, and they can be enhanced by attaching scopes, silencers, or laser sights to them.

The game leads JC to various places all around the globe. The cities he visits, as well as most mission areas, are expansive and fairly open to accommodate different approaches to solving the same problems, depending on the player's preferred style of play. Most of the missions can be tackled in various ways, e.g. with brute force, stealth, or extensive usage of lock-picking and computer hacking abilities. At certain points, the course of the storyline can also be influenced by the decisions made by the player. Similarly to System Shock games, the environment is largely interactive, the player being able to pick up, use, and discard various types of objects.