The film begins as we learn that Superman has been missing for five years. He has traveled to where astronomers believed they had discovered the remains of Krypton. Then Superman returns to Earth, crashing back into his adoptive mother's crop field in a craft like the one that delivered the baby Kal-El. He awakens the next morning reminiscing about his childhood. He returns to the The Daily Planet and his life as Clark Kent in Metropolis. He learns that Lois Lane is now a mother and has won the Pulitzer Prize for her article "Why the World Doesn't Need Superman."
During Superman's absence, Lex Luthor has been released from prison. While away, Superman missed the appeals trial to testify against Lex. Upon his release, he tricks a rich widow into a sham wedding to get his hands on her money. Lex travels to the Fortress of Solitude, steals Kryptonian crystals, and returns to Metropolis to experiment with a tiny fragment. The growing crystal causes a blackout due to an electromagnetic pulse, interfering with the test flight of a new space shuttle tethered to a Boeing 777---a plane which Lois Lane is aboard while covering the story. Clark flies into action as Superman and stops the plane from crashing into a baseball field.
The world rejoices in Superman's return, but Lois is more concerned with the blackout. Clark meets her fiancÚ Richard White, nephew of Daily Planet editor-in-chief Perry White, and their son, Jason. Superman is emotionally hurt when he overhears a conversation between Lois and Richard in which she says she never loved Superman. He buries himself in his work, including halting a bank heist and saving Kitty, Luthor's co-conspirator. While Kitty distracts Superman, Luthor steals kryptonite from the Metropolis Museum of Natural History. Perry assigns Lois to interview Superman while Clark investigates the blackout. That night, Superman arrives at The Daily Planet and takes Lois for a flight, during which he apologizes for leaving her.
After her latest Superman interview, Lois focuses her attention on the blackout again and ascertains its origin. She and Jason sneak onto Luthor's ship, not realizing who owns it, and are captured. Luthor reveals his grand scheme: using one of the stolen Kryptonian crystals to grow a new continental landmass, destroying existing continents, and in the process killing billions of people and leaving him as the world's sole landowner. Luthor inquires as to who Jason's father really is, but after Lois asserts that the father is Richard, he leaves to launch the crystal (now encased in green kryptonite) into the sea. Under water, the crystal begins to create a new landmass. Lois faxes their co-ordinates to The Daily Planet and is attacked by a henchman. The henchman is hit by a piano, appearing as though Jason threw it at him; afterward, Lois and Jason are imprisoned in a galley. Luthor hears of the incident and flees in a helicopter. The landmass's growth causes destruction in Metropolis, to which Superman attends, and Richard arrives in a sea plane to rescue Lois and Jason. Superman arrives to help, and then he flies off to find Luthor, who has returned to the landmass.
Meeting Luthor, Superman discovers the landmass is filled with kryptonite, which weakens him to the point that Luthor and his henchmen are able to beat and torture him. Superman falls into the ocean, after being stabbed with a shard of kryptonite by Luthor. Lois makes Richard turn back to rescue Superman, and she removes the kryptonite from his back. Superman, regaining his strength from the Sun, lifts the landmass by putting layers of earth between him and the kryptonite. Luthor and Kitty escape in their helicopter, but not before Kitty, unwilling to let billions of people die, tosses away the crystals; she and Luthor are stranded on a desert island some time later. Superman throws the landmass into space, but is weakened by the kryptonite and crashes back to Earth. Medical doctors manage to remove more kryptonite from Superman's body, but cannot penetrate his skin with their conventional surgical tools. While Superman remains in a coma, Lois and Jason visit him at the hospital, where, careful not to let Jason overhear, Lois whispers a secret into Superman's ear. Superman later awakens and flies to see Jason, reciting Jor-El's last speech to Jason as he slumbers. Lois starts writing another article, titled Why the World Needs Superman.