Superman II is notably infamous for its complicated production. The original director Richard Donner had completed, by his estimation, roughly 75% of the movie in 1977 before being taken off the project. Many of the scenes were shot by second director Richard Lester, who had been an uncredited producer on the first film. However, in order to receive full director's credit, Lester had to shoot up to 51% of the film which included refilming several sequences originally filmed by Donner. According to statements made by Donner, roughly 25% of the theatrical cut of Superman II contains footage he shot, including all of Gene Hackman's scenes. In 2006, a re-cut of the film was released titled Superman II: The Richard Donner Cut. The new version restores as much of Donner's original conception as possible, with approximately 83% of his footage included. Some of Lester's theatrical footage was retained to fill-in gaps in the story line that Donner had not been able to film before his firing.
Prior to the destruction of Krypton, the criminals General Zod (Terence Stamp), Ursa (Sarah Douglas) and Non (Jack O'Halloran) are sentenced by Jor-El to banishment into the Phantom Zone for insurrection, murder, robbery, manslaughter, gambling, jail break and stolking among other crimes. After traveling through the galaxy for thirty years, the Phantom Zone is shattered near Earth by the shockwave from the harmless detonation of a hydrogen bomb, which had been launched into space by Superman (Christopher Reeve) after foiling a terrorist plot to blow up Paris. The three Kryptonian criminals are freed from the Zone, 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 (which they mistake as being capital city of "Planet Houston" due to NASA's transmissions), the three travel to the White House and force the President of the United States (E.G. Marshall) to surrender to Zod on behalf of the entire planet during an international television broadcast. When the President pleads for Superman to save the Earth, Zod recognizes Superman as "the son of our jailer" and vengefully demands that Superman come and "kneel before Zod!".
Meanwhile, the Daily Planet sends Clark Kent and Lois Lane (Margot Kidder) 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 falls into the room's fireplace, when trying to recover Lois' fallen hairbrush. When Lois discovers that his hand is unburned, 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 parents. Superman declares his love for Lois and wishing to spend his life with her. He decides to transform himself into a human, by exposing himself to Red Kryptonian sunlight in a crystal chamber, giving up his powers to become romantically closer to Lois, despite the pleas of the artificial intelligence of his mother, Lara. After spending the night together, the two return to populated areas by automobile, and learn of Zod's conquest of the world. Realizing that humanity cannot fight Zod themselves, Clark decides to return to the Fortress to try to reverse the transformation.
Lex Luthor (Gene Hackman), who has escaped from prison, finds and infiltrates the Fortress before Superman and Lois arrive, learning of Superman's connection to Jor-El and General Zod. He offers to lead Zod to Jor-El's son in exchange for control of Australia. The three Kryptonians form an alliance with Luthor and go 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 battles the three in Metropolis. Zod realizes Superman cares for the innocent humans, and takes advantage of this weakness by threatening bystanders. To protect the city, Superman flies off towards his Fortress, but Zod, Ursa, and Non pursue, carrying Lois and Luthor (who guides them to the Fortress) follow him. Upon arrival, Zod declares Luthor has outlived his usefulness and plans to kill both him and Superman. Superman tries to get Luthor to lure the three into the crystal chamber to depower them, but Luthor, eager to get back in Zod's favor, reveals the chamber's secret to the villains. Zod forces Superman to seemingly again undergo the process, only to realize too late that Superman, fully expecting Luthor's treachery, had already altered the process to expose everyone outside the chamber to the red light, removing the Kryptonian criminals' powers while leaving his own intact. After easily defeating the trio, Superman returns Luthor to the authorities and flies Lois to her home.
At the Daily Planet the following day, Clark finds Lois upset about knowing his secret. He then kisses her, using his abilities to wipe her mind of her knowledge of the past few days. Later, Clark has a rematch with the truck driver who beat him up earlier and, as Superman, restores the damage done by Zod, replacing the flag on top of the White House.