JC Denton is a nano-augmented agent for UNATCO, the United Nations Anti-Terrorist Coalition. The game begins with the player taking control of JC for his first mission - to single-handedly take care of a terrorist seizure of Liberty Island. JC's orders are to locate the leader of the terrorists, Colonel Leo Gold, to find out information on stolen shipments of Ambrosia, a synthe sized vaccine which is the only known treatment of the plague sweeping the country, known as the "Gray Death". As JC begins to track down the missing Ambrosia, he comes to realize that the policies of UNATCO at times seem barbarous or overly aggressive. His brother Paul, a fellow UNATCO agent, urges JC to use non-lethal force wherever possible, to the dismay of fellow agents and UNATCO Director Joseph Manderley.
JC tracks the stolen vaccine to Juan Lebedev, a wealthy sympathizer to the Northwest Secessionist Forces (NSF), who were responsible for the seizure of the vaccine and the seizure of Liberty Island. Upon reaching Lebedev's private jet, JC encounters Paul, who urges him to spare Lebedev, and insists that the Gray Death, Ambrosia, and UNATCO are part of a global conspiracy by select individuals to take control of the world. Regardless of the player's choice, the missing Ambrosia is seized by UNATCO. JC returns to the headquarters to learn that his brother's killswitch, an emergency countermeasure against rogue agents, has been activated due to his associations with the terrorists. JC is then ordered to Hong Kong, to assassinate Tracer Tong, a hacker who has connections to both Paul and various terrorist organizations. However, JC instead is taken to his brother, who explains his actions and asks for JC's assistance in sending a distress signal to Paul's allies. JC does so, and has his killswitch activated in response. Ultimately, JC is captured after sending the distress signal, and imprisoned in an unknown facility.
A mysterious AI calling itself "Daedalus" contacts JC, and assists in his prison break. The AI informs JC that the facility belongs to the organization known as Majestic-12 (MJ-12), and the facilty is actually located underneath UNATCO's main headquarters. JC escapes his former place of employment, and travels to Hong Kong to get in contact with Tracer Tong, who is the only one who can help deactivate his still active killswitch. After JC assists Tong by putting an end to a major feud between two different groups of Triads, Tong helps deactivate his killswitch and saves JC's life. Tong then sends JC to the VersaLife corporation, an MJ-12 front, to find plans for the Gray Death, and to help put an end to its manufacture. After analyzing the plans stolen from the corporation, Tong determines that the virus was developed in-part by the mysterious Illuminati, who he then puts JC in contact with. Stanton Dowd, a member of the Illuminati, reveals that Bob Page, a former member and current owner of MJ-12 and VersaLife, is responsible for the manufacture and distribution of the Gray Death virus. Page stole the plans for the virus, which was originally intended to be used for augmentation purposes, and converted it into a weapon for his own benefit.
Dowd then puts JC in contact with Morgan Everett, the current leader of the Illuminati and resident of Paris, France. JC first must earn Everett's trust by assisting Silhouette, a French terrorist group, and stealing more information about the Gray Death from a Knights Templar cathedral. Everett then sends JC to Vandenburg to assist X-51, a group of former MJ-12 scientists once stationed at Area 51, who have a plan of attack against Page by integrating Daedalus with restricted military networks. This plan backfires when Page fuses Daedalus with his own AI, Icarus. The two combine to form "Helios", an extremely powerful AI capable of dominating the global communications network. After JC secures plans from an MJ-12 laboratory to build a universal constructor capable of producing mass quantities of Ambrosia, Page attempts to use a nuclear bomb against X-51 and Vandeburg. JC quickly changes the destination of the missile to instead strike Area 51, and Bob Page.
The missile destroys the area around Area 51, but the majority of the facility is underground and sustained little damage. JC works his way through the facility and discovers the truth behind Page's intentions; he sought to control the world by integrating the Helios AI and himself, giving him control over nanotechnology. It is at this point that JC (and the player) must choose what happens to humanity and civilization. Tracer Tong urges JC to destroy Area 51 and Helios, sending humanity to the dark ages but freeing them from corruption and dependence on technology. Morgan Everett asks JC to kill Bob Page and rule the world with an invisible hand as a member of the Illuminati. Helios asks JC to merge, that they may become a supreme being, capable of guiding humanity with benevolent and enlightened rule.
Throughout the game, JC comes off as cold and unemotional (due in part to his extensive nano-augmentation), but is quite intelligent and perceptive. Paul regularly notes JC's independence, quoted as saying "One can be too independent, I'm coming to believe." He is idealistic to a fault, and regularly engages in philosophical conversation about the nature of man and how man should be ruled. However, much of his personality is affected by the player's choices, in both conversation and action.
In DX: Invisible War
JC returns in Deus Ex: Invisible War, albeit not in the starring role. Invisible War combines the three endings of the previous game in order to continue the story, JC fuses with the Helios AI, but the merger is imperfect, causing a catastrophic meltdown which destroys Area 51, and leads to the rise and fall of various groups, including the Illuminati. The unstable nature of JC's merger forces him to be frozen in Antarctica in order to survive, while Paul Denton and Tracer Tong start ApostleCorp in an attempt to perfect a universal biomod structure to save JC, and further their goals of a universal merger with Helios, and thereby a perfect democracy.
Whether or not JC's goal is successful is ultimately dependent on the player. Should the player choose to side with JC, the end result is the collective consciousness and perfect democracy that JC sought to achieve by his merger back in the events of Deus Ex. Alternatively, Alex D has the option of killing JC in order to achieve one of the other endings, so the ultimate fate of JC is unknown at this time.