darkSpyro

While the basic story of the game remains unchanged whether the player opts for the "Good" or "Evil" karma path, there are some story elements that change depending on the player's choice at that time.

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 contains 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, during which he discovers his newfound powers. 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 by government agents. During his arrest, 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, taking the Ray Sphere with him.

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 that the Ray Sphere consumes the bio-energy from those around it and transfers 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 and destroy it. Alden goes on a killing spree while heading into the Historic District. After a long battle, Alden is defeated and jumps off the bridge. During the battle, Alden destroyed huge sections of the bridge. Cut off from the Warren, Cole goes ahead into the Historic District 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, Kessler has arranged for Trish to fall 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.

Cole goes to face Kessler at ground zero of the original explosion. 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 a version of 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 rather than fight, but The Beast eventually caught up to them and killed Kessler's family. Kessler realized the only way to stop the Beast would be to use his powers to go back in time and prepare his past self, Cole, for battle against it as it was too late to fight back in Kessler's time. 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 than in his timeline. Kessler was also the anonymous customer that directed Cole to use it. Kessler used Trish's death as a means to prepare Cole to make the harsh choices in battle with The Beast. After Kessler dies from the battle, Cole declares his hatred for Kessler, but promises that he'll be ready for The Beast.

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.