The game begins with Chicago being destroyed in a terrorist attack. Alex D, the protagonist, and another Tarsus trainee, Billie Adams, along with several Tarsus leaders, are evacuated to another Tarsus Facility. Some time after their arrival, the facility is attacked by forces of the Order Church.
Alex is contacted by Billie, who reveals that she is a member of the Order. She claims that Tarsus is using its trainees as test subjects in a biomodification program, and asks Alex to join the Order.
Once at the Order base in Seattle, he is asked to find out what happened to a group of Order troops sent on a rescue mission to a Tarsus facility. He discovers that they defected to the Knights Templar, who take a more militant approach to matters than the Order.
Over the course of the game, Alex goes on a series of missions for the Order, another organization called the WTO, and another organization called ApostleCorp. During one of the missions, he discovers that he is a clone of JC Denton, a character from the first game with aspirations of creating a perfect global democracy through a bioengineered hive mind. Other missions show him that the organizations he is working for desire to rule the world. ApostleCorp seeks to fulfill Denton’s vision of the future, the Illuminati, who control the WTO and the Order, want to use Denton’s technology to create a benevolent dictatorship, and the Templars want to eliminate biomodification entirely and create a global holy empire.
Near the end of the game, Alex comes into possession of data necessary for any of the factions to take control of the world. Each faction asks Alex to upload the data to their base on Liberty Island. Who rules the world in the end depends on which of the factions the player decides to upload the data to. It is also possible to simply send the data to none of them, instead destroying all of their bases on Liberty Island. This allows another faction, the Omar, to take control of the Earth after allowing the rest of the world to kill themselves off in various wars.
Plot
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The game begins with Adam Jensen in Sarif Industries' Detroit headquarters taking care of security preparations for the company's forthcoming presence at a National Science Board hearing to discuss the need for augmentation technology regulation. Adam's ex-girlfriend Megan Reed will take the opportunity to announce a revolutionary discovery made by her team that will allow people to augment themselves freely without having to resort to anti-rejection drugs, though she is nervous as she fears people will ask about the source of her discovery, a subject referred to as "Patient X." During a meeting between Adam and Sarif Industries' CEO David Sarif, the company is suddenly attacked by a group of heavily armed soldiers led by three heavily-augmented mercenaries. Adam tries to rescue Megan, but is caught by their leader Jaron Namir, who severely injures Adam, and the attackers burn most of the victims in order to make them unrecognizable. Adam survives by undergoing extensive augmentation provided by Sarif. He is called back to action six months after the attack to intervene in a hostage crisis in a Sarif manufacturing plant, which was taken over by the radical anti-augmentation terrorist group Purity First. Inside, Adam encounters an augmented terrorist attempting to steal the Typhoon, an experimental military-purposed augmentation. Upon being found, the hacker shoots himself while pleading for help, apparently forced against his will. Adam confronts the Purity First leader Zeke Sanders, who denies any knowledge about the augmented hacker, leading Adam to believe that Purity First is being manipulated by a third party. Zeke can be killed, captured, or allowed to escape.
After the hostage crisis is resolved, Sarif tells Adam that the police reports do not mention any augmentation on the hacker, indicating a cover-up. Sarif sends Adam to the morgue to investigate the corpse himself and retrieve the hacker's neural hub. Evidence scattered in the police department reveals that both the plant incident and the original attack had crucial pieces of evidence covered up by government official Joseph Manderley. Sarif Industries' cyber-security head Francis Pritchard analyses the hub and discovers that the hacker was a literal "human proxy," controlled by someone else. Pritchard traces the source of the control signal to an abandoned factory complex, which Adam investigates. There, he finds the augmented mercenaries involved in the Sarif attack. Adam descends into the facility and finds a massive underground secret internment camp run by FEMA. Deep inside the facility, Adam fights Lawrence Barrett, one of the augmented mercenaries. After defeating Barrett, Adam demands to know how FEMA is involved, to which Barrett brushes FEMA off as just being used by a higher authority. Barrett gives Adam an address in Heng Sha Island in China before attempting to suicide bomb Adam.
Adam travels to Heng Sha only to find the building mentioned by Barrett under lockdown by the private military company Belltower Associates, the de facto police in Heng Sha. Adam infiltrates the building's penthouse and discovers that it was the residence of the hacker controlling the proxy, Arie van Bruggen. Investigating the apartment, Adam learns that van Bruggen had gone into hiding with the help of another client of his, Triad crime boss Tong Si Hung. At Tong's nightclub, The Hive, Adam learns that van Bruggen is hiding out at a nearby capsule hotel. When confronted, van Bruggen claims he was hired by Zhao Yun Ru, CEO of Tai Yong Medical, Sarif Industries's main competitor, though she's now sent in Belltower to dispose of him, his purpose having been fulfilled. However, van Bruggen had left a compromising recording of Zhao inside the Tai Yong Medical headquarters as an "insurance policy" and enlists Adam to retrieve it, claiming it has the information he requires. After van Bruggen forges a Tai Yong access pass for Adam, Belltower soldiers storm the hotel, prompting the former to hide and the latter to escape.
Adam recovers the recording inside Tai Yong Medical's headquarters, in which Zhao reveals that the Sarif scientists were kidnapped and had their tracking implants disabled, meaning they, along with Megan, could still be alive. She also reveals that Eliza Cassan, the celebrity news anchor of media conglomerate Picus, is also involved. Adam finds and confronts Zhao at her private penthouse but she flees into a panic room and sets off an alarm, forcing Adam to escape. Adam makes his way to Picus headquarters in Montreal to confront Eliza, only to find a hologram instead. Belltower spec ops soldiers storm the building, prompting Adam to make his way to the source of the hologram's signal in a secret sub-basement. There, he discovers that Eliza is actually a self-aware Artificial Intelligence designed to manipulate public perception through the media. Their meeting is interrupted by another of the augmented mercenaries, Yelena Fedorova. After Adam defeats Fedorova, Eliza informs Adam that the scientists' tracking implants were removed by Doctor Isaias Sandoval, the aide of William Taggart, leader of the peaceful anti-augmentation organization Humanity Front and that David Sarif knows more than he appears to.
Adam returns to a riot-torn Detroit, where Taggart is scheduled to give a speech. After mentioning Eliza's claims to Sarif, the latter informs Adam that everything that has happened so far is consistent with the actions of the Illuminati. After publicly confronting Taggart during his televised speech, Adam learns that he was unaware of Sandoval's actions and that Sandoval is also Zeke Sanders's brother. Adam goes to Sandoval's apartment where he finds a secret bunker filled with Purity First members, proving his allegiance to the terrorist group. Adam confronts Sandoval, who reveals that he was unable to remove the tracking implants, so he changed the frequency to avert tracking attempts. Publicly disowned by Taggart, Sandoval attempts to commit suicide, though Adam talks him out of it. Pritchard manages to track one of the implants belonging to Sarif scientist Vasili Sevchenko, to Heng Sha. Nearing his arrival to the island, however, Adam's aircraft is shot down by Belltower, leading to a massive ambush which may result in the death of the craft's pilot, Faridah Malik. Adam discovers that Belltower is on a manhunt for him and that augmentation users all over the world are being advised to have their biochips replaced due to a defect. Adam tracks the signal which leads him to Tong Si Hung wearing Sevchenko's arm, who states that Sevchenko's corpse was sold to his gang by Belltower. Not having any love for Belltower himself, Tong directs Adam to one of Belltower's ships and gives him a bomb to plant as a distraction. When Adam detonates the bomb, he notices that the distraction also allowed Tong's son to escape Heng Sha. Adam then stows away in a high-tech hibernation pod. When Adam wakes up, he finds that he is currently in the Omega Ranch, a biotech research complex in Singapore. Adam finds the three Sarif scientists, who perform a distraction allowing him to access the secure part of the complex where Megan is held. In the secure sector, Adam once again encounters Zhao and confronts her with knowledge gained from the scientists that the Illuminati are creating a "killswitch" for all augmented people worldwide so they will not challenge their rule. After succeeding or failing (depending on if Adam has the new biochip) to use the killswitch on Adam, she orders Namir to kill him.
After defeating Namir, Adam finds Megan who reveals that the facility is owned by Hugh Darrow, a world famous millionaire and the "father" of augmentation technology. Darrow is currently involved with Panchaea, a massive geoengineering facility in the Arctic Ocean designed to stop global warming via iron seeding. She also reveals that the basis of her revolutionary discovery is Adam's DNA, who is unknowingly Patient X. At that moment, while giving a press conference from Panchaea, Darrow activates a signal that causes everyone who got the biochip upgrade to turn violently insane (if Adam got the upgrade, Megan uses a device to isolate him from the signal). Adam travels to Panchaea to confront Darrow. There, Darrow explains that he invented the technology to help the less fortunate, but it has since become just another means for the powerful to exert control over the rest of the world, as well as potentially causing humanity to lose its moral center. Darrow used the insanity-inducing signal as an attempt to get the technology permanently banned, but with the correct augmentation, he can reveal that this is not entirely pro bono - he is ironically one of the few people whose DNA is completely incompatible with augmentations which is why he wears a leg brace. He is thoroughly bitter about being unable to enjoy his creation. Adam races to shut the signal down, encountering Sarif and Taggart along the way who each suggest a different course of action for Adam. Adam later arrives the core of Panchaea, where Zhao merges with the Hyron Project, a hidden bioelectronic quantum supercomputer. Adam successfully destroys Hyron and Zhao, making his way to the broadcast center where he is contacted by Eliza. Eliza explains to him the various options he can take: he can broadcast Darrow's confession about augmentation and the Illuminati thus ensuring that augmentation is permanently banned, he can blame the Humanity Front for the biochip sabotage thus ensuring that augmentation is developed further (Sarif's suggestion), he can blame the event on tainted augmentation anti-rejection drugs thus ensuring tight regulation on augmentations (Taggart's suggestion) or he can set the entire facility to self-destruct, destroying the truth, letting humanity decide for itself. When Adam makes his choice, the game ends, and Adam reflects on how his augments have interfered with his own human nature. Knowing that the whole world could progress the same way, Adam is left either confident, or worried, with the thought of a future in which the human revolution will become significantly less human.
In a post-credits scene, Bob Page is heard talking to Morgan Everett about the "Morpheus project." Megan Reed is revealed to be working for him on a "nanite-virus chimera." It's also implied by the achievement unlocked by viewing the scene ("The D Project") that Adam's DNA will be used as the basis for the creation of the Denton brothers.
tl;dr
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