The story culminates in a choice that determines the future of humanity:
Denton’s first mission involves securing the Statue of Liberty from NSF terrorists. However, he soon discovers that his brother, , also a nano-augmented agent, has defected to the NSF. Paul reveals a terrifying truth: UNATCO is actually a front for a shadow organization called Majestic 12 (MJ12), led by the billionaire Bob Page .
Forced to go rogue to save his brother, JC joins forces with various underground factions: Deus Ex The Conspiracy
The old-world secret society, led by Morgan Everett , who want to regain control of the world from the more radical Bob Page.
A group of former Area 51 scientists who are working on a way to dismantle MJ12's network. The Final Confrontation The story culminates in a choice that determines
Destroy the global communications hub, plunging the world into a decentralized "Dark Age" where humanity is free from global control but must survive without modern technology.
JC eventually infiltrates , where Bob Page intends to merge with an advanced Artificial Intelligence named Helios . This would give him absolute control over all global communications and technology, effectively making him a god. The Three Endings Forced to go rogue to save his brother,
Competing crime syndicates that JC must unite to secure advanced technology.