When Marcus Holloway, a self-taught hacker, is accused of a crime against Blume for hacking he did not commit, he is recruited by DedSec who informs him of Blume's misdeeds with CTOS in Chicago. The story follows after the events of the first game, where the introduction of CTOS 2.0 angers the leader of DedSec, who hence declares war on Blume in San Francisco. The player's mission is to reveal the plan of Blume Corporation with the CTOS. DedSec members, inspired with the works of T-Bone and Aiden Pearce, are determined to take the fight to the enemy.