Pritchard, Sarif’s tech expert, tracks the hacker's signal to a FEMA facility in Detroit, where Jensen encounters the Tyrants again. This lead takes him to the dual-layered island city of .

To save his life, CEO David Sarif authorizes extensive, military-grade augmentations for Adam. Jensen awakens six months later, essentially a cyborg, famously stating, "I never asked for this".

After defeating the final bosses, Jensen is given the choice by Eliza Cassan to decide the world's future:

Jensen travels to Montreal to confront Eliza Cassan, a world-famous news anchor. He discovers Eliza is actually a sophisticated Artificial Intelligence designed by the Illuminati to control public perception and manipulate global media. Part 3: The Missing Link (Integrated DLC)

Stripped of his augmentations, Jensen must escape a secret base, uncovering experiments where Belltower uses human test subjects to develop the "Hyron Project"—a bio-computer that interfaces human brains with machines. Part 4: The Final Confrontation (Singapore & Panchaea)

The Illuminati has distributed a "glitched" biochip to the public, forcing people to get replacements that allow the Illuminati to remotely shut down or control augmented humans.

The story begins at the Detroit headquarters of Sarif Industries, a leader in human augmentation technology. On the eve of a major scientific breakthrough that would end dependence on the drug Neuropozyne, a mysterious group of heavily augmented mercenaries known as the "Tyrants" attacks the facility.

Returning to work, Jensen is sent to a Sarif manufacturing plant taken hostage by "Purity First," an anti-augmentation extremist group. He discovers a hacker with a neural hub who is remotely controlled by a third party, suggesting the attack was more than simple activism. Part 2: The Global Conspiracy (Hengsha & Montreal)