While each game has a distinct story, they are all set within the same world: an Earth of the future which has evolved 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. Once he arrives in Area 51, Denton has the choice between neutralizing technology and plunging the world into a second dark age, allying with the Illuminati, or merging with an advanced AI so as to impose a benevolent dictatorship. 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, including JC Denton: Alex can perform missions for any of them, and eventually becomes able to choose which organization should rule 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. The Fall is a parallel story, set after the spin-off novel Icarus Effect. It follows the story of Ben Saxon, an augmented former British SAS mercenary, who is on the run from his former employers, a group of augmented mercenaries that play a crucial part in the plot of Human Revolution. 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. A disillusioned Adam works with an international taskforce (hinted to be a precursor to UNATCO in Deus Ex) designed to stop the rising wave of terrorism brought on by the disenfranchised and desperate augmented while working to uncover the perpetrators of the events that led to the current state of the world.
Deus Ex takes place in an unspecified near future[a] in an alternate history where real-world conspiracy theories are true. These include speculations regarding black helicopters, vaccinations, and FEMA, as well as Area 51, the ECHELON network, Men in Black, chupacabras (in the form of "greasels"), and grey aliens. Mysterious groups such as Majestic 12, the Illuminati, the Knights Templar, the Bilderberg Group, and the Trilateral Commission also either play a central part in the plot or are alluded to during the course of the game.
The plot of Deus Ex depicts a society on a slow spiral into chaos. There is a massive division between the rich and the poor, not only socially, but in some cities physically. A lethal pandemic, known as the "Gray Death", ravages the world's population, especially within the United States, and has no cure. A synthetic vaccine, "Ambrosia", manufactured by the company VersaLife, nullifies the effects of the virus but is in critically short supply. Because of its scarcity, Ambrosia is available only to those deemed "vital to the social order", and finds its way primarily to government officials, military personnel, the rich and influential, scientists, and the intellectual elite. With no hope for the common people of the world, riots occur worldwide, and some terrorist organizations have formed with the professed intent of assisting the downtrodden, among them the National Secessionist Forces (NSF) of the U.S. and a French group known as Silhouette.
To combat these threats to the world order, the United Nations has expanded its influence around the globe to form the United Nations Anti-Terrorist Coalition (UNATCO). It is headquartered near New York City in a bunker beneath Liberty Island, placed there after a terrorist strike on the Statue of Liberty.
The main character of Deus Ex is UNATCO agent JC Denton (voiced by Jay Franke), one of the first in a new line of agents physically altered with advanced nanotechnology to gain superhuman abilities, alongside his brother Paul (also voiced by Jay Franke), who joined UNATCO to avenge his parents' deaths at the hands of Majestic 12. His UNATCO colleagues include the mechanically-augmented and ruthlessly efficient field agents Gunther Hermann and Anna Navarre; Quartermaster General Sam Carter, and the bureaucratic UNATCO chief Joseph Manderley. Alex Jacobson's character model and name are based on Warren Spector's nephew, Alec Jacobson.
JC's missions bring him into contact with various characters, including NSF leader Juan Lebedev, hacker and scientist Tracer Tong, nano-tech expert Gary Savage, Nicolette DuClare (daughter of an Illuminati member), former Illuminati leader Morgan Everett, the Artificial Intelligences (AI) Daedalus and Icarus, and Bob Page, owner of VersaLife and leader of Majestic 12, a clandestine organization that has usurped the infrastructure of the Illuminati, allowing him to control the world for his own ends.
After completing his training, UNATCO agent JC Denton takes several missions given by Director Joseph Manderley to track down members of the National Secessionist Forces (NSF) and their stolen shipments of the "Ambrosia" vaccine, the treatment for the "Gray Death" virus. Through these missions, JC is reunited with his brother, Paul, who is also nano-augmented. JC tracks the Ambrosia shipment to a private terminal at LaGuardia Airport. Paul meets JC outside the plane and explains that he has defected from UNATCO and is working with the NSF after learning that the Gray Death is a human-made virus, with UNATCO using its power to make sure only the elite receive the vaccine.
JC returns to UNATCO headquarters and is told by Manderley that both he and Paul have been outfitted with a 24-hour kill switch and that Paul's has been activated due to his betrayal. Manderley orders JC to fly to Hong Kong to eliminate Tracer Tong, a hacker whom Paul has contact with, and who can disable the kill switches. Instead, JC returns to Paul's apartment to find Paul hiding inside. Paul further explains his defection and encourages JC to also defect by sending out a distress call to alert the NSF's allies. Upon doing so, JC becomes a wanted man by UNATCO, and his kill switch is activated by Federal Emergency Management Agency (FEMA) Director Walton Simons. JC is unable to escape UNATCO forces, and both he and Paul (provided he survived the raid on the apartment) are taken to a secret prison below UNATCO headquarters. An entity named "Daedalus" contacts JC and informs him that the prison is part of Majestic 12, and arranges for him and Paul to escape. The two flee to Hong Kong to meet with Tong, who deactivates their kill switches. Tong requests that JC infiltrate the VersaLife building. Doing so, JC discovers that the corporation is the source for the Gray Death, and he can steal the plans for the virus and destroy the "universal constructor" (UC) that produces it.
Analysis of the virus shows that it was manufactured by the Illuminati, prompting Tong to send JC to Paris to try to make contact with the organization and obtain their help fighting Majestic 12. JC meets with Illuminati leader Morgan Everett and learns that the Gray Death virus was intended to be used for augmentation technology, but Majestic 12, led by trillionaire businessman and former Illuminatus Bob Page, was able to steal and repurpose it into its viral form. Everett recognizes that without VersaLife's universal constructor, Majestic 12 can no longer create the virus, and will likely target Vandenberg Air Force Base, where X-51, a group of former Area 51 scientists, have built another one. After aiding the base personnel in repelling a Majestic 12 attack, JC meets X-51 leader Gary Savage, who reveals that Daedalus is an artificial intelligence (AI) borne out of the ECHELON program. Everett attempts to gain control over Majestic 12's communications network by releasing Daedalus onto the U.S. military networks, but Page counters by releasing his own AI, Icarus, which merges with Daedalus to form a new AI, Helios, with the ability to control all global communications. After this, Savage enlists JC's help in procuring schematics for reconstructing components for the UC that were damaged during Majestic 12's raid of Vandenberg. JC finds the schematics and electronically transmits them to Savage. Page intercepts the transmission and launches a nuclear missile at Vandenberg to ensure that Area 51 (now Majestic 12's headquarters) will be the only location in the world with an operational UC. However, JC can reprogram the missile to strike Area 51. JC travels there himself to confront Page.
When JC locates him, Page reveals that he seeks to merge with Helios and gain full control over all nanotechnology. JC is contacted by Tong, Everett, and the Helios AI simultaneously. All three factions ask for his help in defeating Page while furthering their own objectives, and JC is forced to choose between them. Tong seeks to plunge the world into a Dark Age by destroying the global communications hub and preventing anyone from taking control of the world. Everett offers Denton the chance to bring the Illuminati back to power by killing Bob Page and using the technology of Area 51 to rule the world with an invisible hand. Helios wishes to merge with Denton and rule the world as a benevolent dictator with infinite knowledge and reason. The player's decision determines the course of the future and brings the game to a close.