Alex was most likely born in 2047, before Majestic 12 had perfected growth acceleration in Area 51. Following the Collapse, Alex lived with their foster parents in Old Chicago (New Chicago being a WTO Enclave). In their youth, Alex enrolled in the Tarsus Academy. Alex's foster parents were killed in 2072, when the powerful faction, the Knights Templar, attacked Chicago. Alex escaped on a Tarsus helicopter to Seattle, along with the other trainees, and some remaining Tarsus personnel.
|"Arrival: brainwaves theta, 6.3 cycles/s. Fatigue, curiosity, stress indicators minimal. Muscle-fiber scan inaccurate — subject did not disrobe. Suggest requiring Chicago subjects to shower before briefing.
Sleep: 2.3 cycles/s, 1.7 cycles/s, 3.0 cycles/s. No dreams. Subject awoken by loud noise."
|— Subject Journal — Alex D, Deus Ex: Invisible War|
At Seattle Tarsus Academy, Alex encounters Klara Sparks, Leo Jankowski, and classmate Billie Adams. When Order Seekers raid Tarsus, Alex is instructed by Billie to make their way to the hidden lab in the Academy, which contain ApostleCorp scientists and biomods. Alex finally leaves Tarsus and is instructed by the Order Church and the WTO, two major enemy factions. Alex is first asked to investigate ApostleCorp scientist Leila Nassif's apartment in Upper Seattle by Billie; and is then ordered by Order High Augur Lin-May Chen and WTO Captain Donna Morgan to go to Lower Seattle, via the Inclinator, to find a pilot to take them to Mako Ballistics. At Mako Ballistics, Denton is ordered by Donna Morgan to investigate the manufacturing of a powerful weapon called the Mag Rail, which is being used by the Templars. After Alex gains the Mag-Rail prototype, they learn that Dr. Nassif left for Cairo, and are asked to follow her there.
At Cairo, Alex resolves the nanite plague, and is instructed by Donna Morgan to destroy the Nassif Greenhouse, which provides food to the hungry, who the WTO are unconcerned about. Alex encounters their leader, Luminon Saman, in the Order Church at Cairo. Billie is with Saman, revealing that she has sided with the Templars. Denton then investigates Templar activity in the Cairo Arcology, and makes their way to Tarsus Cairo, which has also been taken over by the Templars. Alex eventually locates Dr. Nassif in ApostleCorp's Cairo facility, and learns that the leader of the facility, Paul Denton, has been abducted. Chen orders Alex to kill Nassif, and if the order is followed through, they engage in battle with Klara Sparks, who now works for the WTO.
Alex is then instructed to go to Trier, Germany. Here, they encounter 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, and finds Chad Dumier (the leader of the WTO), and Nicolette DuClare (Her Holiness in the Order Church), after rescuing her from the Templars. They reveal themselves to be the leaders of the Illuminati, and the two factions they lead to be merely pawns for world domination. Dumier and DuClare 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. Alex 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 people with biomod infusions can access. Tong pleads with Alex to save JC from Billie, who is on a mission to kill him.
At Antarctica, Alex uses their 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, Alex can choose to kill Billie or leave her alive (she returns at Liberty Island). When Alex escapes from 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. At Cairo, Alex is blackmailed by Dumier into complying. Alex 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). Alex has the option of rescuing her or leaving her to die. They are then confronted by all three factions (Illuminati, Templars, and ApostleCorp) in the Arcology. Denton is ordered by Saman to give their blood (which will be used to eradicate biomods), by JC to revive Paul and by Dumier to cut Paul's life support. Whichever action Alex chooses will affiliate them with one of the factions, although they are still free to switch sides later in the game. Alex is then taken to Liberty Island, and is placed in a showdown between all three factions, as well as the Omar AI collective. Alex makes their way to the UNATCO HQ ruins, where the Aquinas Hub protocol (the protocol responsible for the centralization of global communications twenty years previously) is stored. Alex is then ordered by the three factions to set up the protocol for their own use. Whichever faction Alex chooses to set up Aquinas for is the faction they side with in the endgame.
- Alex is the only protagonist of the Deus Ex series that does not wear sunglasses.