Opening titles reveal Superman has been missing for five years after astronomers believed that they had discovered the remains of Krypton. He returns to Earth with his spacecraft crashing back into his adoptive mother's crop field and awakens the next morning reminiscing about his childhood. He returns to work as Clark Kent at The Daily Planet in Metropolis, where he learns 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, conned a rich widow into a sham wedding to get his hands on her money, and stolen Kryptonian crystals from the Fortress of Solitude. Luthor returns to Metropolis and experiments with a tiny fragment in a pool which grows to immense size. The growing crystal causes a blackout, interfering with the test flight of a new space shuttle tethered to a Boeing 777 — a plane which Lois Lane is aboard, covering the story. Clark flies into action as Superman and stops the plane from crashing into a baseball field.

Superman (Brandon Routh) tries to save a Boeing 777.

The world rejoices in Superman's return, but Lois is more concerned with the blackout. Clark meets her fiancé 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 a museum. Perry assigns Lois to interview Superman whilst Clark investigates the blackout. At night, Lois goes out for a smoke on top of the The Daily Planet and Superman takes her for a flight, during which he apologizes for leaving her.

Superman (Brandon Routh) and Lois Lane (Kate Bosworth) glide above Metropolis.

After her latest Superman interview, Lois focuses her attention on the blackout again and ascertains its origin. Lois 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 landmass, even though he is aware it will destroy already existing continents and kill billions. He also inquires as to who is the father of Jason after noticing Lois' reaction to the kryptonite being near her son. Luthor launches the crystal (now encased in green kryptonite) into the sea, causing a chain reaction resulting in its massive growth. Lois faxes their co-ordinates to The Daily Planet and is attacked by a henchman. Jason throws a piano at him in an apparent display of super strength, after which Lois and Jason are imprisoned in a galley. Luthor hears of the incident and flees in a helicopter. The landmass' growth causes destruction in Metropolis, to which Superman attends, and Richard arrives in a sea plane to rescue Lois and Jason from the ship, which splits in half and sinks with them trapped inside. Superman rescues them and he then flies off to find Luthor, who has returned to the landmass.

Meeting Luthor, Superman discovers the landmass is filled with kryptonite, which allows Luthor and his henchmen to beat and torture him. Luthor stabs Superman with a shard of kryptonite, after which he falls into the ocean. Lois makes Richard turn back to rescue Superman, and she removes the kryptonite shard from his back. Superman regains consciousness, gathers more energy from the Sun, and lifts the landmass, made of kryptonite-infused earth, by putting layers of earth between him and the kryptonite to protect him from it. Luthor and Kitty escape in their helicopter, but not before Kitty tosses away the crystals; she and Luthor are stranded on a desert island some time later. Superman throws the landmass into space, but, weakened by the kryptonite, crash-lands in Metropolis. The doctors cannot penetrate his body with their medical equipment but manage to remove the rest of the kryptonite from his wound. While Superman remains in a coma, Lois and Jason visit Superman at the hospital, where, careful not to let Jason overhear, Lois whispers a secret in Superman's ear. Superman later awakens and flies to see Jason, reciting his father's last speech to him as he sleeps. Lois also starts writing another article, entitled Why the World Needs Superman.