Alex Denton

Alex Denton was a clone of JC Denton, and by extension, of Paul Denton. He or she was therefore the third Denton "sibling". Alex can be male or female, but for simplicity's sake, the rest of this article will refer to Alex as male.

History
Using game evidence, the webmasters of the website Theos Ek have theorised a plausible version of Alex's history. He was most likely born in 2047, before Majestic-12 had perfected growth acceleration in Area 51. In order to conceal Alex's existence from JC Denton, a hologram of a fully-grown Denton clone was placed in a stasis tank in Area 51. In reality, Alex was only five years old at the time of JC Denton's return to A51.

Following the Collapse, Alex lived with his foster parents in Old Chicago (New Chicago being a WTO Enclave). As a young man, he enrolled in the Tarsus Academy. His foster parents were killed in 2072, when the powerful faction, the Knights Templar, attacked Chicago. Alex escaped on a Tarsus helicopter, which took him, the other trainees, and some remaining Tarsus personnel to Seattle.

Seattle and Mako Ballistics
At Tarsus Seattle, Alex encounters Klara Sparks, Leo Jankowski and classmate Billie Adams, all of whom play a significant role in the game later on. When Order Seekers raid Tarsus, Alex is instructed by Billie to make his way to the hidden lab in the Academy, where he encounters ApostleCorp scientists and biomods for the first time. When Alex finally leaves Tarsus, he is instructed by the Order Church and the WTO, two major enemy factions, and this continues for much of the game. He is first asked to investigate ApostleCorp scientist Leila Nassif's apartment in Upper Seattle by Billie. He is then ordered by Order High Augur Lin-May Chen and WTO Captain Donna Morgan to go to poor Lower Seattle, via the Inclinator, to find a pilot to take Alex to Mako Ballistics. At Mako Ballistics, Alex is ordered by Donna Morgan to investigate the manufacture of a powerful weapon called the Mag-Rail, which is being used by the Templars. After Alex gains the Mag-Rail prototype (which he keeps) and plans, and learns that Dr. Nassif left for Cairo, Alex is ordered to go to Cairo.

Cairo
At Cairo, Alex resolves the nanite plague, and is instructed by Donna Morgan to destroy the Nassif Greenhouse, which provides food to the hungry, whom the WTO are unconcerned about (this is an optional mission). He encounters their leader, Luminon Saman, in the Order Church at Cairo, and Billie is with Saman, indicating her siding with the Templars. He then investigates Templar activity in the Cairo Arcology, and makes his way to Tarsus Cairo, which had also been taken over by the Templars. He eventually locates Dr. Nassif in ApostleCorp's Cairo facility, and learns that the leader of the facility, Paul Denton, had been abducted. Chen orders Alex to kill Nassif, and if he does so, he is engaged in battle with Klara Sparks, who now works for the WTO.

Trier
Alex is then instructed to go to Trier, Germany. Here, he encounters the leader of the local ApostleCorp facility, Tracer Tong. Tong reveals that JC's merge with Helios was unstable, and JC had to be put into suspended animation at Antarctica. He also reveals ApostleCorp's intentions (the biomodification of humanity) and its founder (Paul Denton). He further goes on to reveal the technology of biomod infusions, key to mass biomodification, which Paul tested on himself, but rejected. Paul had to be frozen to save his life, and was abducted by the Templars. Tong gives Alex a perfected biomod infusion, which Alex's body accepts.

Alex then goes to the Black Gate Ruins, where he finds Chad Dumier (the leader of the WTO) and Nicolette DuClare (Her Holiness in the Order Church). They reveal themselves to be the leaders of the Illuminati (from the first game), and the two factions they lead to be merely pawns for world domination. The two try to convince Alex that their leadership is preferable to ApostleCorp's objectives. Alex then finds Dr. Nassif in ApostleCorp Trier (if she was left alive in Cairo), who reveals that Alex is the clone of JC and Paul. He then learns from a Gray working at the facility, as well as Tracer Tong, that there is a portal that leads directly to Antarctica, which only persons with biomod infusions can access. Tong pleads with Alex to save JC from Billie, who is on a mission to kill JC.

Antarctica
At Antarctica, Alex uses his biomod architecture to complete the merge between JC and Helios, which revives JC. In one of JC's memories (Alex had to go through a series of JC's memories to fix the merge), Alex encounters Billie. Here, the player can choose to kill Billie or leave her alive (she returns at Liberty Island). When he escapes Billie, and fixes JC, JC revives, and reveals his plans to Alex in their entirety. He then orders Alex to return to Cairo to rescue Paul. Here, Alex also learns that Ava Johnson (one of the two pilots who flies Alex) is actually an AI construct whose purpose was to pick up JC at Area 51, but never had the opportunity, hence her interest in Alex.

Return to Cairo
At Cairo, Alex is blackmailed by Dumier into complying. He learns that Klara Sparks is held hostage by none other than Donna Morgan, who is told about the Illuminati and accepts the status quo (unlike Lin-May Chen). The player has the option of rescuing her or leaving her to die. Alex is then confronted by all three factions (Illuminati, Templars and ApostleCorp) in the Arcology. He is ordered by Saman to give his blood, which will be used to eradicate biomods. He is ordered by JC to revive Paul. He is ordered by Dumier to cut Paul's life support. Whichever action the player chooses will affiliate him/her with one of the factions.

Liberty Island
Alex is then taken to Liberty Island, where he is placed in a showdown between all three factions, as well as the Omar AI collective. Alex makes his way to the UNATCO HQ ruins, where the Aquinas Hub protocol (the protocol responsible for the centralization of global communications in Area 51 in the first game) is stored. Alex is then ordered by the three factions to set up the protocol for their own use. Whichever faction he chooses to set up Aquinas for is the faction Alex sides with in the endgame.

Endgame
If the player chooses to side with ApostleCorp, Alex is ordered by Paul and JC to step into their infusion chamber in their Statue base, which will distribute Alex's perfected nanites to every human being on the planet, which leads to a peaceful "posthuman civilization".

If the player sides with the Templars, Alex is ordered by Saman to kill the Dentons. Alex's blood and biomod architecture are then used to eradicate biomods, and after years of eliminating modern technology, the world is thrust into a Medieval setting.

If the player sides with the Illuminati, the Illuminati gains control of all communications, and operates the world economy and society in secret, through Aquinas and a mysterious entity called "Ophelia".

The player can also opt to side with none of the three factions, and instead be ordered by the Omar (through Leo Jankowski who assimilated) to kill the leaders of the three factions. This leads to decades of constant warfare which destroys all of humanity, save the Omar.