When a solar flare erupts, Jon Kent manifests superpowers and learns from his mother, Lois Lane, that his father, the missing Daily Planet reporter Clark Kent, was secretly the superhero Superman. Jon begins his attempts to follow his father's footsteps as the new Superman. To find out the truth of his father's disappearance, Jon helps a terrorist organization, led by Pete Ross and Lana Lang, and discovers that his father has been held in an underground facility. Jon frees his father from his captivity, and the Kent family joyfully reunite. During Superman's absence, Lex Luthor has taken control of the Justice League as well as many other aspects of life in America. The Justice League's liaison to Lex Luthor, the Martian Manhunter, is told to recruit Superman into the League once again. When Superman voices his disapproval of Pete Ross and Lana Lang's terrorist methods, his son tells him not to be so hard on them, and also says he is not proud of who his father is. Pete and Lana find the spacecraft that carried Superman to earth, and use it to decode a Kryptonian message they found at the facility where Superman was being kept. Superman finds out everything in the Fortress of Solitude has been stolen, while Batman finds out Wonder Woman is funding the terrorists. Pete Ross threatens to expose Lex Luthor as the man responsible for holding Superman captive, and agrees not to reveal the information in exchange for two hundred million dollars. In addition to the two hundred million dollars, Pete gives Lex one of the advance armors the terrorists used for their operations.
An army of men wearing these armors, led by a man who appears to be Superman, destroys the Statue of Liberty. The Justice League is ordered to bring in Superman, but Batman, Superman and Jon successfully defeat them, with the help of Wonder Woman. They find out Lex Luthor has uses the stolen Kryptonian technology and Superman's genetic to give himself superpowers, but only succeeded in gaining half of the Man of Steel's abilities. Because of his anger built up from all the years of growing up without his father, Jon confronts Luthor alone. Jon initially fares poorly against Luthor, but eventually gains an upperhand and Luthor is defeated. Wonder Woman later forces Pete and Lana to turn themselves into the authorities. The Justice League retires from fighting crime to "spend more time with their families." Bruce Wayne, no longer donning the cape and cowl of Batman, decides to pursue presidential candidacy to restore democracy to the country. Jon Kent finally establishes a relationship with his father, and continues his career as a superhero.
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