Deus Ex

=== Setting and characters ===
Deus Ex takes place in the year 2052 in a dystopian cyberpunk future on the brink of social and economic collapse, where multiple conspiracy theories and organizations are real. The two main factions in-game are the Illuminati, portrayed as an ancient secret society controlling civilization from the shadows, and Majestic 12, once subordinate to the Illuminati and now a splinter group. During the events of Deus Ex, the world is being ravaged by a plague dubbed the Gray Death, with supplies of its Ambrosia vaccine limited. The game takes place across multiple locations including multiple parts of the United States (New York City, California, Nevada), Hong Kong, and Paris. A recurring location is Liberty Island, which houses an operating base for the United Nations Anti-Terrorist Coalition (UNATCO). UNATCO's main conflict is with the National Secessionist Force (NSF), a terrorist group targeting Ambrosia shipments. Another feature of the world is "augmentations", artificial enhancements using mechanics and nanotechnology.
The main protagonist is JC Denton, an agent for UNATCO who has received advanced nanotechnology; he works at UNATCO with his brother Paul Denton, who shares the same nanotech augmentations, under the command of Joseph Manderley. Other important characters are Tracer Tong, a hacker allied with the Triads of Hong Kong; Morgan Everett, a high-ranking Illuminati member; Daedalus, an artificial intelligence construct and its successor Icarus; Walton Simons, newly appointed Administrator of the Federal Emergency Management Agency (FEMA); and Bob Page, a corporate CEO and current leader of Majestic 12.

Plot

Note: While the general plot of Deus Ex follows a distinct path, many elements are subject to the player's decisions. The game also offers subplots that the player may or may not encounter, depending on their actions within the game. This synopsis concentrates on the main, unavoidable plot thread of the game.
JC Denton is brought straight from training when the NSF attack Liberty Island. While he defeats them, a shipment of Ambrosia is stolen and taken to New York. JC takes on multiple missions tracking the NSF and the Ambrosia shipment, eventually finding out that Paul has defected to the NSF, acting as a mole within UNATCO after learning the Gray Death was a man-made disease used for power and population control. As punishment for his defection, Simons takes control and activates a kill switch, giving Paul just 24 hours left alive. Ordered by Manderley to eliminate Tracer Tong in Hong Kong, JC instead finds Paul's hideout in New York, learning more details about UNATCO's operations but prompting his employers to attack him. JC's kill switch is also activated, and Paul can either escape or be killed by Simons' agents.
JC is taken to a Majestic 12 prison beneath UNATCO, but escapes with help from "Daedalus", initially assumed to be a hacker. JC travels to Hong Kong and finds Tong, getting help removing the kill switch in exchange for resolving a war between the Triads. Tong identifies the virus as created by VersaLife, Page's company and a former Illuminati asset. Destroying the universal constructor creating the virus and stealing the Ambrosia plans, JC is then sent by Tong to the Illuminati's remaining base in Paris. JC finds Morgan Everett, who explains the Gray Death was intended as an aid to augmentation, but was stolen and repurposed by Page and Simons. To stop Page from producing more Gray Death, JC agrees to defend against Simons's assault on Vandenberg Air Force Base, where a group of Majestic 12 defectors are hiding with a second universal constructor.
JC learns from the Vandenberg scientists that Daedalus is an AI currently allied with Everett. When Everett attempts to defeat Majestic 12 using Daedalus, Page counters with his successor AI Icarus. The process causes Daedalus and Icarus to merge into a new entity "Helios", which seizes control of worldwide communication. JC must then travel to Area 51, where Page is in the process of merging with Helios to gain global power. JC is then given three options for defeating Page and resolving the situation. Tong wants the base destroyed, bringing down the world's communication network and triggering a "Dark Age" of free city states, Everett wants to preserve the technology and re-establish the Illuminati as the world's controllers, and Helios seeks to merge with JC and become a benevolent dictator.