Summary of Novel
At the end of Deus Ex: Human Revolution, Cyborg private security officer Adam Jensen failed to prevent a shadowy organization from causing every Transhuman on the planet to go into a fight-or-flight response and attack anyone near them. After the destruction of Panchaea, he wakes up in facility 451 run by World Health Organization in Alaska located in the Kenai Peninsula. He was greeted by two doctors named Rafiq and Mcfadden, who told Adam that he just woke up from a coma. During his time at the facility Jensen befriends with Harrison Stacks Stacker, an ex-steeplejack from Seattle, and notices that some things are not as they seem at the aforementioned facility.
Six days later, an agent from Homeland Security named Jenna Thorne arrived and interrogates Adam about his part of the Aug Incident when Panchaea collapsed. After some questioning, he admits vaguely he was in Panchaea and tried to stop Hugh Darrow and but refuses to answer concretely because he doesn't trust Thorne.
Meanwhile, Meanwhile, in a hotel in Sorrento, Italy, Elizabeth DuClare and Lucius DeBeers discuss Janus, their latest adversary. DuClare tells DeBeers that she has formulated a plan of action to uncover Janus. She states that she and DeBeers "will need to play a subtle and lengthy game" in order get close to Janus.
Thorne discloses Adam's presence in Panchaea at the time of Incident to other augmented residents of facility 451 which goads them to start a fight with Adam after they broke Stacks's nose. Adam, with the help of Stacks, managed to fend off others before the facility guards intervene the fight. After realizing things will get only worse for him and Stacks in the facility once they were at Thorne's mercy, Adam hatched a impromptu plan and spontaneously escaped the facility with Stacks by breaking out of the surrounding fence and steal a truck.
Adam and Stacks then drive to an abandoned gas station in Soldotna. Once there, Adam easily contacts Francis Pritchard because they were out of facility 451's signal jamming range. Because Adam's status was officially listed dead as he was presumably missing after the destruction of Panchaea, Pritchard is hesitant to trust the caller. However, after Adam exchanges some facts and snide comments with Pritchard, the hacker agrees to help them steal another truck at the station. Adam then orders it to be driven back to Detroit.
After they arrive in Detroit, Pritchard meets with them. He takes a DNA sample of Adam, which confirms his identity. On a monorail, Pritchard tells that David Sarif got away from Panchaea but his submersible was damaged, causing him severe nitrogen narcosis. He was put in a coma "sleeping through most of everything that came after." Sarif Industries declared bankruptcy and was bought up by Tai Yong Medical while Sarif was still in his coma. Pritchard does not know Sarif's current whereabouts but knows that Sarif did not take the news well when he woke. Pritchard also tells that he has had to accept hacking gigs to earn his living since Sarif Industries bankrupted.
After the monorail ride, Pritchard leads Adam and Stacks into the Rialto movie theatre which now functions as Pritchard's living quarters. It also becomes apparent that Motor City Bangers now dominate those turfs. A banger called Cali tells Pritchard that his hacking skills have been noted and MCB leader Magnet craves more favors. Adam and Stacks intervene, making Cali retreat. Inside the theatre, Stacks suffers symptoms from Darrow Deficiency Syndrome. Adam decides they three will break into ex-Sarif HQ towers in hope of finding Neuropozyne for Stacks, who previously gave his last cup of it to an augmented person in the Detroit aug-ghetto camp. For Adam, it's also about catching up with the recent past since his awakening in facility 451.
At the same time, in the US division of Task Force 29 in California, Jim Miller informs Christian Jarreau and Raye Vande about military-grade augmentations that are about to leave US soil from Detroit. He suspects they will end up in hands of John "Sheppard" Trent.
Adam, Pritchard and Stacks break in through the underground car park connecting to Sarif Towers, with Adam destroying a Boxguard in process which distress signal TF29 notices in their base of Detroit operations and the recording prior to Boxguard's destruction. Pritchard explains Tai Yong left only robots to guard the building. After they get into the Testing and Quality control department, Stacks gets a post-traumatic stress reaction after seeing loose leg and arm augments. Adam calms him down and they get Stacks some Neuropozyne. Adam then scans himself and finds a foreign chip in his augmented right arm, plucks it out and crushes it. Scavengers and homeless people then enter into their position. Adam orders Pritchard to open rest of the storages to let the scavengers take the rest relenting them. A homeless person then informs Adam about armed thugs at Milwaukee Junction, ex-manufacturing plant of Sarif Industries. They turn out later to be Motor City Bangers.
Meanwhile, at a virtual meeting of the Juggernaut Collective, Janus informs other members of the Collective that Adam has resurfaced. Janus and another member makes the case for utilizing Jensen for benefit of the Collective. Janus confirms that he will set things in motion toward this goal.
Back at the Rialto theatre, Pritchard discloses to Adam explaining he's noticed an organized pattern raiding and looting Sarif facilities implicating something else is going on. Adam realizes military-grade not-for-sale augmentations may end up in wrong hands and determines to make it stop. Despite Pritchard's warnings he takes Stacks with him to Milwaukee Junction.
Stacks and Adam plan to destroy the Junction with a gas leak and remote-detonating explosives. At their way of getting out, Stacks gets another stress reaction when entering a room full of augmented limbs, which alerts nearby MCB members. Bangers then wound Stacks lethally, who confesses at his last moments he killed his family at the time of Incident leaving only their limbs left when Darrow's signal stopped broadcasting explaining the stress reaction at Sarif HQ. Adam then runs when he smells stench of the gas. Stacks detonates the explosives before he dies. Angered at Stacks's death, Jensen chases down Magnet on the roof, who refuses to give tangible answers about who he is working for (Pritchard noticed Magnet used Infolink to get orders from somewhere else). Magnet escapes as Jensen is distracted by the sounds of the Task Force closing in. At the spotlight of a Task Force helicopter, Pritchard then creates another distraction allowing Adam to escape through sewers.
Back at the Rialto theater, Adam meets with Alejandra Vega, who held Pritchard at gunpoint before Adam arrived and Garvin Quinn. They offer Jensen information in exchange for Juggernaut Collective co-operation. Pritchard is suspicious but Adam is listening. At this time members of Task Force 29 has been able to identify the person they chased on the roof and the destroyer of the Boxguard at Sarif Headquarters as Adam Jensen. They are unsure what to think about Jensen but they intend to interrogate him when given the chance.
Meanwhile, in-flight above Switzerland, DuClare receives an incoming transmission from DeBeers. DeBeers tells her that a source embedded in Interpol has informed him that Task Force 29 is currently investigating Adam Jensen in Detroit. DuClare had lost face to DeBeers due to Adam's escape from the Alaska facility, which was nominally under her control. DeBeers tells DuClare that they must take a firm hand to bring the situation under control. After the conversation, DuClare commands her data tablet to conduct a search on "'White Helix Lab, subset project name Black Light."
Back in Detroit, Adam then heads to Spector's Tavern after learning from Pritchard his pass card has been used in raiding Sarif facilities. He confronts an ex-Sarif Security guard Henry Kellman about this. Kellman reveals Donald Wilder as his boss. Wilder is another ex-Sarif Security employee. Soon, Cali and two other Bangers storm the Tavern killing other customers, bartender Jake and Henry. Adam kills the other bangers and tears away with his nanoblades all Cali's four augmented limbs before Pritchard locates Wilder. Adam leaves before the police arrives.
Adam breaks in Wilder's apartment without setting off alarms. At gunpoint, Wilder admits he helped Bangers to steal the mil-spec augments but he then turns the tables by shooting a P.E.P.S. pulse from his augmented arm towards Adam triggering the EMP mine immobilizing him. As he is about to kill Adam, Wilder gets a call ordering him not to kill Adam. He then calls the police impersonating Adam before knocking him unconscious. Task Force 29 captures Adam before Detroit Police is able to do the same. Agent Vande tells that their technicians noticed the caller used a voice-changer device so they know it was not Adam. At the interrogation he agrees to co-operate with the Task Force.
Jenna Thorne meets with Don Wilder in Yukon Hotel. Thorne is displeased the way Wilder handled with Kellman, stating that the mission might be compromised. She then shoots Wilder with a silenced pistol before he even gets a grip of his revolver. Thorne then warns Magnet and DuClare about the changed situation.
Adam comes to the airport initially as an observer with rest of the Task Force 29. He is able to recognize Magnet from the crowd. John Trent is recognized as the primary target. As Vande's team reaches the jet and kills a Banger, Sheppard activates an autocannon, which shoots agent Lund who was dragging an EMP to disable the jet and any other person near the aircraft. Adam then takes a jeep and starts driving it towards the jet. Magnet attacks Adam and grips from the hood. Adam dispatches him quickly and then reaches jet's rear part and releases the cargo hold while the jet is on air and falls to the ground, and was knocked unconscious upon hitting the ground.
Adam eventually recovers and Jarreau tells Adam that he has potential to be employed by Task Force 29. Jarreau also reveals that the augments that Sheppard failed to extract are planned to be moved by a train to a military base where they will be destroyed. They also dropped any charges against Jensen and allows him to leave their custody as a sign of good faith.
Agent Thorne is contacted by an Illuminati superior (unnamed but hinted to be De Beers). Her superior informs her that her assignment of ensuring extraction of the augmentations from Detroit remains incomplete. Thorne points out that Adam has complicated her task, only to be told by her superior that Adam's involvement is not her concern and that she is "not the only asset in play." Her superior then states that a team of operatives will be deployed to retrieve the augments, which are needed for operations in Europe. Thorne is then given the assignment to take command of the operatives to retrieve the augmentations.
Pritchard contacts Adam about Wilder's corpse which is to be taken to a furnace as infectious material according to Detroit Police department. Adam suspects something valuable is on the corpse. Pritchard hacks into traffic grid which allows Adam carjack the vehicle carrying the corpse. On a safe position assisted by Pritchard he accesses Wilder's eye augment and its last recording learning in horror that agents of the Illuminati is about to hit the train carrying the augments.
Adam hides himself in a Lucky Dot convenience store, wondering how he could warn the Task Force agents about the impending attack. A few moments later, someone hacks into a service robot and reveals himself as Quinn, and he informs Adam that he can help Adam with his dead end. Janus has found out the course of the train carrying the augments, and Alex can fly him to it. Adam then gets to Alex's VTOL as fast as he could. During the flight, Quinn also informs Adam that the Juggernaut Collective believes that Task Force 29 has been compromised by the Illuminati, and that the Illuminati manufactured the reason for bringing about the Task Force so they could sow the seeds of a military organization (hinted to be the UNATCO) to serve their needs. Vega states that Adam would make a good agent to infiltrate and investigate the Task Force.
Before Adam gets to the train, Thorne's team is already inside and has killed several members of the Task Force. Adam clears his way toward Vande, and is confronted by Thorne. Thorne indicates her desire to kill Adam, but an extensively augmented German trooper, unnamed but suggested to be Gunther Hermann, tells her that killing Adam is not the orders. Vande assists Adam in temporarily escaping to another part of the Train. Thorne orders Gunther to kill Adam and Vande. Gunther reluctantly complies, but he tells Thorne that she will be held responsible for acting outside of orders. Gunther attacks Adam and gains the upper hand, but Adam is able to destroy the train's controls, pushing the train into overdrive, which will cause the train to explode when it crosses the state border. Gunther weighs his options and opts to flee instead of continuing to fight Jensen and get caught in the explosion. Already injured by an earlier gunshot from Thorne, the near-to-death Raye Vande is finished by Thorne slicing her throat. Adam in turn kills Thorne with his Typhoon augmentation and was rescued in time by Vega and Quinn just before it explodes.
Jarreau arrives with additional members of his Task Force and finds Adam at the south of Granger, Indiana, as the only survivor of the ambush by Thorne's team. Jarreau tells Adam it was Vande who sold them out with new upcoming evidence about it. Adam knows already it is not true because he witnessed her saving his life and attacking Thorne and also not showing any marks of lying on his Social Enhancer augmentation but knows also there is nothing he can do to repeal the set-up of Vande.
Later, Adam decides to join the Juggernaut Collective, stating he's had enough of innocent lives cut short by Illuminati.
In Geneva, Switzerland, DuClare is contacted by DeBeers. DeBeers states that the operation in Detroit has been an utter mess, and that valuable assets have been lost. DeBeers says that due to the loss of the augmentations shipment, they will need to find an alternate supplier. In response, DuClare states that she will accelerate their other plans. Filled with anger, DuClare ends the conference call, and opens her files on the "Black Light" project. On the screen, a dead man's face looks back at her.
At a Juggernaut Collective meeting, a member reports that Adam has agreed to join them. Janus informs the Collective members that the heart of the Illuminati's infiltration of Task Force 29 is in Eastern Europe, specifically Prague, and that Adam is the best option for investing the task force's unit in Prague and its local commander, James Miller. Janus also states that he "understands" Adam, and that Adam will help the Collective bring down the Illuminati, or perish in the attempt.
Adam meets one last time with Pritchard in the Rialto. Pritchard gives Adam a pocket secretary where he has gathered all the data for two years what he and Adam have experienced and gone through. The book closes with Pritchard responding to Adam's mission statement of stopping Illuminati as You make it sound like the end of the world, to which Adam replies: "Not yet, but you can see it from here."