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.

The Game of the Year Edition of Deus Ex adds multiplayer with the brand new Deathmatch and Team Deathmatch modes. It also features a new editing software kit, giving users the possibility to create levels (both for single- and multiplayer) or edit existing levels. Finally, it also contains a full CD soundtrack featuring 30 remixed songs from the game.