Whether you start your story off playing Good or Evil the ending remains the same, there is just a few little elements that change.
The story begins with the main protagonist Cole delivering a package from an anonymous customer to the Historic District and then was told to open it. Little to his knowledge inside the package was the Ray Sphere which activated as he opened the package and took out six city blocks. Cole survived the explosion and is nursed to health by Trish, as he is recovering he discovers his new powers. When the Voice of Survival blames Cole for everything that has happened the whole city turns against him, including Trish, whose sister was killed in the blast.
Cole and Zeke tries to escape the quarantine city but fails by the overwhelming government agents. Captured, Cole is givin instructions by Moya a high ranking government agent, to return to the Empire City, recover the Ray Sphere and her husband John, if both tasks are accomplished they can leave the quarantine city. Cole agree's and make's his way through the city turning on power to districts in order to fight the gang's that are trying to take control. As he interacts with Sasha, Alden, and Kessler, the leader's of these gangs, he learns that Kessler displaced Alden from the leadership of the First Son's an organized crime group, and initiated construction of the Ray Sphere. After rejecting Sasha's attempt at romance, Cole is able to defeat Sasha and capture Alden, but during a break out by the dust men at the prison, Zeke's own heroism antic's caused Alden to break free, which greatly irritated Cole.
Cole and Zeke track down Alden, who has recovered the Ray Sphere; Cole was able to distract Alden long enough so Zeke could grab the Ray Sphere. Zeke is now caught between Alden and Kessler, thinking he could gain power's like Cole, Zeke activate's the Ray Sphere endangering the entire city again, but this time nothing happens. Kessler figure's out what's wrong and offer's Zeke power for assisting to repair the Ray Sphere. Zeke agrees and leave's with Kessler.
Cole finally is able to track down John and finds out that he is neither FBI or Moya's husband but instead a NSA agent that was involved in the creation of the Ray Sphere. John explains that the Ray Sphere absorb's the bio energy from the people around it and transfer's the power to the one holding the Ray Sphere, granting him super power's at the cost of thousand's of peoples live's. John urge's Cole to find it and destroy the Ray Sphere so it can do no more harm to the people of the city. Alden is on a killing spree at the Historic Disctrict, after a long battle Alden jumps off the bridge. Because of the battle the bridge had been greatly destroyed. Cut off from the Warren, Cole goes into the Historic Disctrict.
While searching for the Ray Sphere, Kessler had kidnapped Trish and six other doctors, and force's Cole to choose between her and the six doctor's. Regardless of your choice Trish still fall's to her death, but is briefly revived by Cole. If the player has Good Karma, Trish will be proud of Cole and confesses her love to him, but if the player has Evil Karma Trish will curse Cole's name with her dying breath.
Cole then work's with john to recover the Ray Sphere. The player get's the decision to destroy the Ray Sphere or use it, if you use it you gain more power and get red and black electricity, whatever your desicion John dies anyway from the Ray Sphere malfunctioning and he get's disintegrated.
Cole then goes to Ground Zero, (where the first explosion happened that gave Cole his power's) to fight Kessler. As the battle begin's Zeke tries to get involved but just get's tossed aside by Kessler. Cole eventually mortally wounds Kessler. With his last action Kessler implant's Cole with his memories, revealing that Kessler is Cole in a future alternate timeline. In that timeline Cole (Kessler) was married with children to Trish, but soon the appearance of the entity known as "The Beast" brough the entire world to chaos. Kessler took his family and flead, but eventually The Beast caught up to them and kill's Kessler's family. Realizing the only way to stop The Beast was to use his power's to go back in time and prepare Cole for battle against The Beast, Kessler seized control of the First Sons from Alden, Manipulating then shunning Sasha's advances due to his past love for Trish, and ordered the construction of the Ray Sphere much earlier than in his timeline. Kessler was also the anonymous person that instructed Cole to deliver and open the package. Kessler also used Trish's death as a means to making sure Cole could make the impossible decision while fighting The Beast. Kessler then dies and Cole declare's his hatred for Kessler saying "when the time comes, I will be ready."
The ending now depends on your Karma, if you have good karma the city will continue to rebuild itself and praise you as there hero, but if you have Evil Karma the city will now be fully plunged in to utter chaos. Cole will then realize he is the strongest person in the city and declares Kessler an idiot, and laughs at the idea of using his powers to fight The Beast.
