Prior to the destruction of Krypton, the criminals General Zod, Ursa and Non disable a security guard at a crystalline matrix table. The general removes a red spire from the table and destroys it; the thunderclap as the piece is shattered resonates through the city and sets off a trap that ensnares the three brigands. The red spire's destruction is clearly an act of treason, and for this and other crimes they are sentenced by Jor-El for banishment into the Phantom Zone.
Many years after traveling through the galaxy, the Phantom Zone is shattered near Earth by the shockwave from the harmless detonation of a hydrogen bomb launched into space by Superman. The three criminals are freed, finding themselves with super powers granted by the yellow light of Earth's sun. After attacking human astronauts on the moon and the small town of East Houston, Idaho, the three travel to the White House and force the President of the United States to surrender to Zod (on behalf of the entire planet) during an international television broadcast. When the President warns Zod that Superman will stop them, Zod announces his demand for Superman to come and "kneel before Zod!"
Prior to Zod's arrival, Clark Kent and Lois Lane are sent on assignment for the Daily Planet to Niagara Falls. Lois becomes suspicious that Clark is Superman and tries to lure him into revealing his identity by throwing herself into the Falls, but Clark manages to save her with subtle use of his powers. That night, Clark accidentally reaches into the room's fireplace to recover his glasses after he trips; when Lois discovers his hand is not even burnt, Clark is forced to admit he is Superman. He takes her to his Fortress of Solitude near the North Pole and shows her the traces of his past stored in the energy crystals of the Fortress, one of which is the green crystal that created the Fortress and opened Superman's contact with his long-deceased parents. Lois misplaces the green crystal under her purse. Superman decides to undergo a transformation to make himself human by exposing himself to the red Kryptonian sunlight to become romantically closer to Lois, despite Lara's warnings. The process that destroys many of the energy crystals, except the green crystal, lying a considerable distance away. After spending the night together, the two return to populated areas by conventional means, and soon learn of Zod's demand. Realizing that humanity cannot fight Zod themselves, Clark decides to return to the Fortress to try to reverse the transformation.
Lex Luthor, who has managed to escape from jail (with Eve Teschmacher's assistance), has tracked down the Fortress using an alpha wave detector, and infiltrated the Fortress before Superman and Lois arrived, learning from the crystal of Superman's mother of Superman's connection to Jor-El and of General Zod. He traces Zod to Washington, D.C., and offers to lead Zod to Jor-El's son in exchange for control of Australia. Accepting his offer, the three Kryptonians are directed by Luthor to the offices of the Daily Planet where they abduct Lois. Superman arrives, after having found the green crystal and reversing the transformation process, and attempts to fight the three. Zod realizes Superman cares for the innocent humans and take advantage of this weakness to force Superman into submission. To protect Metropolis, Superman flies off towards his Fortress, with Zod, Ursa, and Non giving chase and carrying Lois and Luthor with them.
At the Fortress, Superman attempts to lay one last trap to stop Zod but fails. As Zod holds Superman in submission, Luthor reveals the ability of the Fortress to revert Superman into a human, a punishment that Zod sets forth. Luthor himself initiates the process by placing the green crystal in the remaining control panel. When Superman steps into the transformation chamber, the rest of the Fortress is bathed in red light. The three villains realize too late that Superman, knowing of Luthor's treachery, altered the transformation process by means of the green crystal to expose everyone outside the chamber to the red light, thus removing Zod, Ursa and Non's Kryptonian powers. With Lois' help, Superman is able to send the criminals into the bottomless depths of the Fortress. Superman returns Luthor to the authorities, despite the criminal's pleas that he was in on his plan. Superman returns Lois to her home. At the Daily Planet the following day, Superman (as Clark) kisses Lois, using his telepathic abilities to wipe Lois' mind of all the events surrounding Zod's arrival on Earth including her knowledge that Clark and Superman are the same person. Superman restores the damage done by Zod, and as he replaces the flag on top of the White House, promises the President to never again abandon his duty.