The game ends when Kessler dies and Cole proclaims, "When the time comes, I will be ready." He had set the events of the game into motion by ordering the construction of the Ray Sphere as well as passing it to Cole for him to cause the explosion. Kessler reveals his motive for the events throughout the game telling Cole that he was preparing Cole for an eventual battle against an entity known as "The Beast" who had destroyed Kessler's world. Kessler duels Cole in a battle to the death and it is eventually revealed after Kessler is mortally wounded that he is in reality a version of Cole from the future of an alternate timeline. Regardless of the choice, Cole will eventually come face to face with Kessler, the leader of The First Sons, the organized crime group in the city who had seized control of the city after the quarantine. Cole eventually obtains the Ray Sphere and the player is given the choice to either destroy it or use it. The game follows Cole's journey to obtain the Ray Sphere in order to escape from the quarantine as part of a deal he made with an FBI agent during his failed escape attempt at the start of the game. After the explosion, the city was quarantined by the government causing organized crime groups within the city to seize control of Empire City from the local authorities. The Ray Sphere is an object of great power as it is able to consume the energy of the people around the user and transfer that energy to the user, making him immensely powerful at the cost of thousands of lives. Set in 2009, The game explains the origins of Cole MacGrath, a bike courier, who gained his electrical-based superpowers after surviving a large explosion in Empire City caused by the package he was carrying containing the Ray Sphere.
In the first two games and the spin-offs, the player controls Cole MacGrath, later in the third game as Delsin Rowe and Abigail "Fetch" Walker, as they freely roam around the city, fighting crime or creating havoc along the way.