While each game has a distinct story, they are all set within the same world: an Earth of the future which has evolved into a dystopian cyberpunk society. In this setting, several organizations compete for overall control of the world. Several of the societies mentioned or shown are inspired by real-world and invented secret societies and conspiracy theories. The one constant through the series is the Illuminati, although FEMA, Majestic 12, and the Knights Templar are also featured. The main characters in the series possess artificially acquired superhuman abilities, referred to as "Augmentation."
Deus Ex takes place during 2052, while the world is facing a crisis caused by a mysterious nano-virus called the Gray Death. In the midst of the crisis, JC Denton, a nano-augmented rookie agent for the United Nations Anti-Terrorist Coalition (UNATCO), is sent to eliminate terrorist cells, but ends up drawn into the various schemes of rival factions and secret societies, who are responsible for the epidemic. Invisible War takes place twenty years later, after a massive economic depression and period of war called the Collapse that was indicated by Denton's actions and a combination of possible events from the first game. The game's protagonist, Alex D, a clone of Denton, is drawn into a conflict between two seemingly opposing factions, and learns of conspiratorial factions which seek to drastically change the world.
Human Revolution is set in 2027, twenty-five years before the first title, where corporations have extended their influence past the reach of global governments and the development of bio-mechanical augmentation by a few elite and powerful companies threatens to destabilize society. The game follows Adam Jensen, the security chief for bio-tech company Sarif Industries. After a devastating attack on Sarif's headquarters which leaves him near-death, Adam is forced to undergo radical augmentation surgery, and he becomes embroiled both in the search for the attackers and the political and ethical repercussions of augmentation technology. Mankind Divided is set in 2029, 2 years after the events of Human Revolution in a world dealing with the consequences of the previous game's events. Regardless of the choice made by Adam at the end of Human Revolution, the Illuminati have twisted his message and augmented individuals are persecuted and feared.