Following the events of Chicago, San Francisco becomes the next city to install the CTOS (central Operating System), which connects everyone with everything. Marcus Holloway, an intelligent hacker from Oakland, California, is punished for a crime he did not commit by the upgraded CTOS 2.0 system, which categorizes him as the suspect. Realizing the system covertly brings harm to the innocent citizens of San Francisco, he decides to work with the hacking group DedSec to take down the city's CTOS 2.0, and Blume, the main company behind it.
Marcus joins DedSec and works with the fellow hackers Sitara, Wrench, Horatio, and Josh, and they begin using their skills to expose corrupt organizations and corporations that are secretly using stolen personal CTOS data for their own personal gain. The game begins with Marcus' DedSec initiation test: deleting his own CTOS profile from the database. Being successful, he is accepted into DedSec. He is soon alerted about a fake church called New Dawn that serves as a criminal organization. Eventually, Marcus stumbles upon the existence of Bellwether, a data manipulation program being fed CTOS data by Dušan Nemec, Blume's CTO, to manipulate world finance and politics. DedSec later manages to recruit the assistance of old-time hacker Raymond "T-Bone" Kenney, who is determined to battle Blume.
