About

Cole is instructed by an anonymous customer to deliver a package to a location in the Historical District, and then to open it; unbeknownst to Cole, the package contained the Ray Sphere, which activates upon opening and wipes out six city blocks. Cole manages to survive the blast and is nursed back to health by Trish. When the Voice of Survival pinpoints Cole at the center of the explosion, the city turns against him, and Cole and Zeke try to escape the quarantine with Cole's new powers but are overwhelmed. Cole is convinced by Moya to return to Empire City to seek out the Ray Sphere and her husband John in exchange for Cole and his friends' release from quarantine. Cole proceeds to follow Moya's missions, restoring power to the city to be able to fight off the various gangs that have taken over. As he comes to interact with Sasha, Alden, and Kessler, he learns that Kessler displaced Alden from the leadership of the First Sons and initiated construction of the Ray Sphere, while rejecting Sasha's attempts for romance. Cole is able to defeat Sasha and capture Alden, but during a breakout attempt by the Dust Men, Zeke's own heroism antics allow Alden to go free, much to Cole's irritation. Later, Cole and Zeke track down Alden, who has recovered the Ray Sphere; Cole is able to distract Alden long enough for Zeke to recover it. However, Zeke realizes that he could gain superpowers himself through the Sphere and attempts to activate it, but nothing happens. At that moment, Kessler shows up and offers to help Zeke fix the Ray Sphere to gain powers. Zeke agrees and departs with Kessler.

Cole is finally able to track down John, but learns that John is neither from the FBI nor Moya's husband, but instead an undercover NSA agent who assisted in the creation of the Ray Sphere. John explains the Ray Sphere consumes the bio-energy from those around it and transfer that power to the person holding it, granting them super abilities at the cost of thousands of lives, and urges Cole to help him find it and destroy it. As they search, Cole discovers that Kessler has kidnapped Trish along with six other doctors, and forces Cole to choose between saving her or the other doctors. Regardless of the player's choice, Trish falls to her death, but is briefly revived by Cole. If the player has good karma, Trish will be proud of Cole and profess her love, while if the player has bad karma, she will curse his name with her dying breath. After mourning for his loss, Cole works with John to discover the Ray Sphere; the player can opt to destroy it or use it to further enhance Cole's powers, but either option causes the Ray Sphere to malfunction, disintegrating John. Choosing to use the Ray Sphere will result in Cole being infamous and unchangeable.

Cole goes to face Kessler at ground zero. As they fight, Zeke appears and tries to intervene but is tossed aside by Kessler. Cole eventually mortally wounds Kessler, and tries to seek answers for Trish's death from him. Kessler uses his last actions to implant memories into Cole's mind, revealing that Kessler is Cole from the future of an alternate timeline. In that timeline, Cole (as Kessler) and Trish were happily wed with children, but soon the appearance of an entity known as "The Beast" plunged their world into chaos. Kessler and Trish fled with their children, but The Beast eventually caught up to them and killed Trish and their children. Kessler realized the only way to stop the Beast would be to use his powers gained by the Ray Sphere to go back in time and prepare his past self, Cole, for battle against it. Kessler seized control of the First Sons from Alden, shunning Sasha's advances due to his past love for Trish, and ordered the construction of the Ray Sphere much earlier in his timeline and was the anonymous customer that directed Cole to use it. Kessler further used Trish's death as a means to prepare Cole to make the harsh choices in battle with The Beast. As Kessler dies from the battle, Cole gets Kessler's last message transported into his brain, and tells himself that he'll be ready when The Beast comes.

The ending of the game depends on the player's karma. If the karma is good, Cole considers what the future holds, still lamenting the loss of Trish and the strain on his friendship with Zeke, while the city works at rebuilding itself, idolizing Cole as its savior. If the player's karma is evil, Cole recognizes himself as the strongest person alive with the failing Empire City for his taking.