|"The legendary video game franchise, which PC Gamer called "The Best PC Game of All Time," comes to comics in advance of the highly anticipated new installment in the series! Adam Jensen is a cybernetically enhanced security operative for the powerful Sarif Industries in a future where biological enhancements have become commonplace, yet fanatically opposed by many. While recovering the kidnapped niece of the founder of Sarif Industries, Jensen unstitches a mystery that goes all the way back to his fully human SWAT origins in Detroit – and an adventure of violence and betrayal that will span the globe!"|
|— Synopsis, DC Comics|
The issue begins in Juarez, Mexico in 2027 AD. The setting is a safe house for a Mexican drug Cartel with several armed guards, under the guise of a meat supplier for the "Hot Shot Burger" fast food chain. An unknown, but apparantly augmented assailant drops several guards without sounding an alarm. Meanwhile, inside one of the houses on the compound, a young woman identified as Nina Freeman is tied to a chair. She is missing several fingers, her wounds are infected, she is in shock and dehydrated. Alexander Kronstadt, an enforcer for the Stolchinaya Mafia Clan, is threatening to maim her once more when the unknown infiltrator bursts through the ceiling and stabs Kronstadt's "surgeon" through the wrist, just before he is able to do any more harm to Nina. There is a short gun battle and fist fight as the infiltrator, who turns out to be Adam Jensen, kills or disables five more of Kronstadt's men. Kronstadt kneels behind Nina, using her as cover and holding a gun to her head. He demands that Jensen put his pistol down or he'll kill Nina. Jensen obliges, but is too fast when Kronstadt tries to shoot him, using the dead thug he was holding by the neck as a body shield to stop Kronstadt's rounds. He then tackles Kromstadt and kills him with a nano-blade protracted from his forearm. He then goes to untie Nina, but she demands that she not touch him, calling him a freak.
Later, on approach to Sarif Industries in Detroit, Faridah Malik is discussing the mission with Jensen. She tells Jensen that he is not a machine, though he is still uncertain about how he feels with his new extensive augmentations. Faridah tells Jensen not to stop thinking, because thinking is what makes him human.
On the helipad at Sarif Industries, Natalie Freeman, Nina's mother and David Sarif's sister, is waiting to be reunited with her daughter. Sarif is there and attempts to console Nina and mentions that he wants to be part of her life now, but is immediately admonished by Natalie, saying that Nina being kidnapped is his fault. Sarif promises 24-hour security for the both of them, along with prosthetic augmentations for Nina, but Natalie says that "scars are part of being human, not something to be ashamed of." Sarif explains that he was only trying to help, because they are family, but Natalie accuses him of throwing away his humanity like it was something to be ashamed of. Natalie and Nina leave, telling Sarif to stay away from them. Sarif apologizes to Jensen for having to see the scene, explaining that some people can't accept progress. Jensen replies that some people didn't have a choice.
Later, in the Detroit L.I.M.B clinic, Dr. Vera Marcovic tells Jensen that she's impressed with his physical recovery after his augmentation, citing that there is no sign of implant rejection. She expresses concern over Jensen's psychological state, and asks him if he's still having dreams. He deflects the question, saying that he only has good dreams. Marcovic presses him further, but he resists, saying that he doesn't need psychological evaluation. Marcovic continues to insist that, given what he went through in the Sarif Incident, Jensen is at risk for many psychological issues. Jensen assures her that he is "not that deep."
After his checkup, Jensen is back at Sarif HQ, discussing the break-in at the Sarif Manufacturing Plant and the attempted theft of the Typhoon Explosive System by Purity First, a pro-human terrorist organization, with Sarif and Francis Pritchard. Sarif wonders if the group that kidnapped his niece is behind it, but Jensen doesn't think so, hypothesizing that the Russian Mafia Families were only taking advantage of Sarif Industries while it appeared to be weak after the break-in. Jensen wants to pursue a lead that they have with FEMA, but Sarif orders Jensen to pursue the location provided by Lawrence Barrett before he died, saying that the recent happenings are bigger than government corruption.
At a Humanity Front demonstration in Detroit, William Taggart is giving a speech denouncing augmentations, citing several negative consequences, such as augmentation psychosis, of augmentation. A heavily augmented man is slinking through the large crowd. He stops at a point in the speech and detonates a rudimentary version of a Typhoon, killing dozens. He then goes on to slaughter some of the survivors, including a Picus reporter. After killing the reporter, the bomber uses the reporter's blood to draw a bull's eye on the camera, and says "Deus Ex."