What the letters "JC" stand for is never revealed in either game. According to Harvey Smith, an idea was considered during development that the character would be a descendant of Jesus Christ. Warren Spector stated in an interview that the player was originally to be able to choose the gender of the character, with the ambiguity of J.C. being a "nice, unisex name" to flow with Denton. Although the feature was not implemented, the name was left unchanged.
JC has solid, bright blue eyes as a result of nano-augmentation to enhance his night-vision, which he obscures by wearing sunglasses. In the PC-version his hair and skin color can be chosen by the player at the start of the game from a pre-generated set; changes made to JC's appearance affect those of Paul as well.
JC's origins are muddled in the game. In Area 51, a datacube reveals JC's date of inception as March 17, 2054, with an "assigned birth date" of March 17, 2029. Since Deus Ex takes place in 2052 this would mean JC is physically 23 years old (this is supported by the fact Morpheus mentions JC is 23), and he was growth accelerated to his biological age. This would be assuming that the inception date was incorrect. This leaves no room for most of his original backstory, unless the acceleration was somehow irregular or his memories are in fact false (which raises serious questions about his relationship with Paul). Another datacube contains an email about "creating genetically viable candidates for nano-augmentation through cloning", speculating that "in the future, this process could be streamlined through the application of accelerated growth and memory implantation", which lends some credence to this theory.
This leaves open the possibilities that JC and/or Paul are the result of such a process (and that all references to their past and their parents are forged) or that the datacube with JC's age (and the appearance of fully-grown clones in tubes) is simply an inconsistency introduced by development of the game. Given the complexity of the plot of Deus Ex and its numerous twists, neither can be discounted.
JC Denton is revealed to be sharp, intelligent and perceptive, yet cold and stolid and a bit of a loner. This is in contrast to his brother, who is passionate and empathic. In an early conversation with his brother, he states that he is "used to being on (his) own" after Paul fondly remembers his UNATCO initiation ceremony. Paul then wryly remarks that "one can be TOO self-sufficient". However, JC is also highly idealistic and believes his work in UNATCO to be heroic and for the greater good. JC's personality is, however, largely down to the player, as the game gives the ability to carry out whatever action he or she desires, whether it be morally reprehensible or admirable, or anywhere in between.
JC is a clone of his older brother Paul Denton (thus, he is referred to as the "Secondary Unit" by Bob Page and Walton Simons and why Morpheus makes no mention of Paul as a relative) and a prototype created by shadowy organization Majestic 12 to test their nano-augmentation program. As a result of screening, Paul was found to have the right combination of biological and genetic factors to make him a good candidate for the nano-augmentation program. To create more compatible test subjects, Majestic 12 produced clones of Paul, but most failed to accept the augmentations. His parents, however, were infertile after Paul's birth. They approached MJ12 looking for a method to have a new baby. MJ12 offered one, in the form of the implantation of an embryo. This procedure produced a clone of Paul, which would later become JC Denton. Paul and JC are, thus, identical twins born eleven years apart. However, later on in the game, it is shown that a third clone (revealed to be Alex Denton in the sequel of the game) was being constructed in a tank filled with liquid and wires going into its body. This is presumably either the growth acceleration procedure carried out by MJ12 or the nano-tech augmentation embedding for the subject.
Later, as Paul reached adolescence, he became more independent and MJ12 decided to have him and his parents killed, while JC was sent to a Swiss school where he could be more closely supervised. Paul escaped this attack, and JC grew up unaware of his early childhood with Majestic 12. After graduation, JC joined UNATCO, United Nations Anti-Terrorist Coalition.
JC's first assignment after joining UNATCO is to track down the barrels of the plague vaccine Ambrosia stolen by the NSF. On his way to the final barrel, he discovers that Paul had been working with the NSF. The player is then given the choice whether to assassinate the NSF leader Juan Lebedev, leave it to Anna Navarre, or kill Navarre and save Lebedev. Whatever his decision, JC ultimately chooses to side with the NSF, and transmits a warning signal to Paul's allies. (Whether Paul survives the repercussions of his and JC's betrayal is up to the player, however given his appearance in Invisible War, it can be said that canonically Paul survives.) JC's "killswitch" is then activated and he is imprisoned by Majestic 12, but quickly escapes with Jock to Hong Kong where his killswitch is deactivated by Tracer Tong.
After settling the conflicts between the Triads in Hong Kong and destroying the Universal Constructor in the VersaLife facility, JC is dispatched by Tong to New York, where he scuttles the superfreighter carrying the Gray Death virus. The previous owner of the ship, Stanton Dowd, instructs JC to track down his Illuminati associate Morgan Everett in Paris, who in turn sends JC to Vandenberg Air Force Base where a group of ex-Majestic 12 scientists were working on a cure for the virus with their own Universal Constructor. After the UC is brought online, the rogue artificial intelligence Daedalus and the MJ12 construct Icarus merge to create a new entity, Helios. JC finishes the UC by uploading the final software component from the computer system of an undersea Majestic 12 base. After diverting a MJ12 missile launch against Vandenberg, JC goes on to Area 51, where Helios, Tong and Everett give him his options for changing the world using the advanced technology in the base. The player can choose to merge with Helios and give the AI's almost limitless power the advantage of human compassion, overload the antimatter reactors and destroy Area 51, crippling the world's communications systems (and destroying Helios), or kill Bob Page but preserve the equipment in the base, giving the Illuminati the power to rule the world in secret.
JC Denton also appears as a CPU-controlled opponent in the mobile game Lara Croft's Poker Party, along with several other characters from games published by SCi/Eidos.