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Paul Denton was born in 2018 to an unnamed couple. When Paul was five, Majestic 12 scientists determined that his physique and genetic makeup were the most suitable for the nano-augmentation project. His immune system was excellent and he had no allergic reactions to non-biological foreign materials in his body. He also had no predispositions to myopia, obesity or heart disease and he was highly intelligent. Since Paul himself was considered too valuable to experiment on, Majestic 12 scientists created a number of clones of Paul in an attempt to find the "sweet spots" in the brain that would allow the clones to control nanites and receive information. Meanwhile, Paul started to grow up, blissfully unaware of the experiments being carried out in his name. When JC (a cloned embryo of Paul) was born, the two were raised as brothers under the careful and clandestine scrutiny of Majestic 12. Their parents never knew that the children were identical twins born eleven years apart.
When Paul was 17 and JC was 6, it was becoming clear that Paul was a bit too unpredictable and independent for Majestic 12's tastes and sent JC into a special Swiss school (actually a front for Majestic 12) where his development could be more carefully controlled. To that end, they arranged to have their parents killed, their death was covered up as a car accident.
In 2040, at the age of 22 years, Paul joined UNATCO and formed a team with agent Anna Navarre, whom he disappointed on several occasions due to his disdain for killing people. Although Paul was busy with his duties at UNATCO, he still visited JC as often as he could. In 2050, Paul accepts an offer of nano-augmentation from UNATCO (secretly through Majestic 12), becoming the first successfully nano-augmented human.
Paul starts as a seemingly pro-UNATCO character who appears frequently, giving JC his UNATCO mission objectives. When JC reaches Hell's Kitchen, he discovers that Paul has been issuing tear gas to the troops instead of ammunition. To compound this strange behavior, when JC returns to UNATCO HQ, he realizes that Paul had failed the raid on the NSF warehouse and was fired.
Further on in the game at Juan Lebedev's private hangar, JC finds out that Paul works for the NSF and he attempts to persuade JC to join, but UNATCO discovers Paul's treachery through JC's infolink, as Alex Jacobson explains. MJ12/UNATCO activates Paul's killswitch, eventually rendering him nearly immobile, so he returns to his apartment in Hell's kitchen and is forced to remain there in pain. The now former UNATCO pilot, Jock, is told to take JC to Hell's kitchen, as Paul needs JC's help. Once there, Paul tells JC to send a distress signal to the Silhouette leader Chad Dumier and to other NSF bases regarding evidence of a conspiracy between UNATCO and MJ12 stored on a datacube nestled in the NSF HQ. When JC sends the signal, Walton Simons tells the troops to kill JC.
Once JC returns to the apartment to take Paul to Tracer Tong in Hong Kong to deactivate the killswitch, MJ12 and UNATCO troops storm the apartment, which leads to Paul's death if JC escapes out of the window or Paul's survival if JC stays with Paul through a firefight out of the front doors of the 'Ton hotel. As with other plot-centric, non-player characters, Paul remains invincible in the fight if the latter choice is made.
Later, if JC helped Paul out of the attack, he encounters him in the medical lab of the MJ12 complex beneath UNATCO HQ, where Paul tells JC about the explosive killswitch of mechanically-augmented soldiers like Anna Navarre and Gunther Hermann, which is activated by uttering a single phrase (killphrase). JC again encounters Paul after arriving at Tong's base in Hong Kong, following the destruction of the universal constructor at VersaLife, where Paul will say that he is recovering, but due to his present state, he cannot be of help. It is revealed that Smuggler helped Paul to get to Hong Kong. If JC escaped out of the apartment window and did not stay with Paul in the MJ12 attack, he will come across Paul's corpse in the same MJ12 medical lab within UNATCO HQ.
When JC finally reaches Area 51, Paul communicates via JC's Infolink and a holocomm at the base. In both cases, Paul encourages JC to trust his conscience and make his own choice as to who he should follow in the endgame.
Though he was the one who convinced JC that UNATCO was the pawn of a global network of conspirators, he has been reluctant to accept the decisions of his brother that led to the conspiracy’s demise and, with it, the Great Collapse of civilization. He is more inclined to blame people rather than systems for society’s troubles, yet gradually he has come to support a new vision for society that JC has been working on in isolation for twenty years. He even volunteered for what should have been the final test of the technology key to JC’s plan, with disastrous results.
Paul founded ApostleCorp with Tracer Tong, the organization centered around the ideals of the merged JC/Helios, in other words, the biomodification of mankind. ApostleCorp developed biomod infusions, enhancements akin to augmentations, and planned to distribute these infusions worldwide, enhancing people without them knowing it. These infusions were tested on Paul, but Paul's body violently rejected the infusion, so he had to be cryogenically frozen to avoid dying. At some point, Paul was abducted by the Templars during a raid on the ApostleCorp's Cairo facility. If the player (Alex Denton) chooses to side with the Templars in the second Cairo mission, Paul will be detained at the Statue of Liberty in the final mission. If the player sides with the Illuminati, the player is ordered to kill Paul by cutting off his life support. Otherwise, Paul can be revived.
The player encounters Paul again on Liberty Island. If he is detained, you have the option of rescuing him. Otherwise, you will find him in the Statue base with JC. He, along with JC, tries to convince Alex to send the Aquinas Hub protocol hidden in the UNATCO HQ ruins (the computer protocol used for global communications at Area 51 in the first game, and now necessary for nanite distribution worldwide) to ApostleCorp, and if the player agrees, Paul and JC then ask Alex to step into their infusion chamber at their home-base in the rebuilt Statue so that Alex's nanites (now perfected) can be distributed globally. If the player refuses, Paul and JC try to kill Alex.
- Even if you save Paul at the 'Ton Hotel by killing all the MiBs, Paul's death will still be triggered if you still decide to exit through the window.
- "This isn't a training exercise, JC. Your targets will be human beings. Keep that in mind."
- "I wish I could have come. At the time I could have cared less that Mom and Dad came to mine, but it was a good thing. The U.N. threw a dinner in honor of me, the first nano-augmented agent."
- "You can relax, JC. I told the troops to stand down."
- "I wish I had an answer for you, but you'll have to decide for yourself who you can trust."
- "Quit screwing around!"
- "Enough! You have a job to do."
- "You got to have God clearance to know...the nanites can be programmed for exponential growth."
- "I'm afraid that's classified."
- "That wasn't funny!"
- "Jesus Christ, JC!"
- "It's only a matter of time before someone clever and ambitious figures out that the tools of dictatorship have been ready-made by well-meaning governments all over the world."