Taking place 70 years after the events in Deus Ex, Invisible War reveals a futuristic world where basic needs are left unmet. It is a world on the brink of chaos after the dismantling of the mighty biotech corporations, a world where multiple religious and political groups now lust after power. Thus begins the sequel to 2000's critically acclaimed first-person shooter, which finds players investigating the different factions struggling for control to determine which groups are beneficial and which are a threat. Enhancements to the core engine include a retooled physics system, refined AI, added character animation, and more choices on the part of the player.

As in the original game, the style of play helps shape the game as it progresses, from how characters interact with the protagonist to the types of situations encountered. Each potential conflict can be resolved in a number of ways, through peaceful means or through violence, using stealth or a show of force. Characters can once again outfit their bodies with an array of biotech parts, some of which include the ability to see through walls, disappear from radar, regenerate from critical hits, or jump 40 feet in the air. The non-linear story takes players from Seattle to remote locations in Cairo and Antarctica.