As the film begins, we learn that Superman (Brandon Routh) has been missing for five years, having traveled to where astronomers believed they had discovered the remains of Krypton. Thereafter Superman returns to Earth, crashing back into his adoptive mother's corn field in a craft like the one that delivered him to Earth when he was a baby. He returns to the The Daily Planet and his life as Clark Kent in Metropolis. There, he learns that Lois Lane (Kate Bosworth) has won the Pulitzer Prize for her article Why the World Doesn't Need Superman.
During Superman's absence, Lex Luthor (Kevin Spacey) has been released from prison. Upon his release, Lex marries a rich widow and obtains her fortune upon her death. Lex then 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 by an electromagnetic pulse, interfering with the test flight of a new space shuttle tethered to a Boeing 777—occupied by Lois Lane who is covering the story. Clark flies into action as Superman and stops the plane from crashing onto a baseball field.
The world rejoices in Superman's return, but Lois is more concerned with the blackout. Clark later meets her fiancé Richard White (James Marsden), nephew of Daily Planet editor-in-chief Perry White, and their son, Jason. Clark is emotionally hurt when he overhears a conversation between Lois and Richard in which she says she never loved Superman. He therefore buries himself in his work, proceeding to halt a bank heist and saving Kitty (Parker Posey), 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 this interview, Lois focuses her attention on the blackout again and ascertains its origin. She and Jason steal onto Luthor's ship, not realizing who owns it, and are captured. Luthor reveals to them his grand scheme of using one of the stolen Kryptonian crystals to grow a new continental landmass in the Northern Atlantic Ocean that will destroy much of Earth's existing continents, in the process killing billions of people and leaving him as the new landmass' owner. On observing the effect of a Kryptonite sample on Jason, Luthor asks who Jason's father really is; 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 Luthor's new landmass. Lois faxes their co-ordinates to The Daily Planet and is attacked by a henchman. The henchman is hit by a piano, which seems to have been pushed at him by Jason; afterward, Lois and Jason are imprisoned in a galley. Luthor flies in his helicopter to the still forming continent. Meanwhile, Superman is attempting to minimize the destruction in Metropolis caused by the new landmass' growth when Richard arrives in a sea plane to rescue Lois and Jason. Superman soon arrives to help and then flies off to find Luthor.
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 him. Superman is stabbed by Luthor with a shard of Kryptonite and falls into the Ocean. Lois makes Richard turn back to rescue Superman, whereupon she removes the Kryptonite from his back. Superman, after 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; Kitty, unwilling to let billions of people die, tosses away the crystals that Lex stole from the Fortress of Solitude. She and Luthor are stranded on a desert island when their helicopter runs out of fuel. Superman pushes the landmass into space, but is weakened by the Kryptonite present and crashes back to Earth. Doctors remove more Kryptonite from Superman's wound, but after it is removed they cannot penetrate his skin with their surgical tools. While Superman remains in a coma, Lois and Jason visit him at the hospital where 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 sleeps. Lois starts writing another article, titled “Why the World Needs Superman". Superman reassures her that he is now back to stay, and flies off to low orbit, where he gazes down at the world.
In February 2006, Warner Bros. announced a summer 2009 theatrical release date for a sequel to Superman Returns. Legendary Pictures was to co-finance Superman: Man of Steel 50/50 with the studio, with Bryan Singer directing. Singer planned to have more action sequences, with the "New Krypton" landmass that was floating in space at the end of Superman Returns to be part of the storyline. Superman was also going to fight "an enemy with real physical power." Production was halted for many reasons, including Singer deciding to make the movie Valkyrie before Man of Steel, screenwriters Michael Dougherty and Dan Harris leaving the project, and the 2007–2008 Writers Guild of America strike, which moved the release date to 2010.
Warner Bros. then decided to reboot the film series. Studio executive Jeff Robinov plans to have the film released either by 2010 or 2011, explaining "Superman Returns didn't quite work as a film in the way that we wanted it to. It didn't position the character the way he needed to be positioned. Had Superman worked in 2006, we would have had a movie for Christmas of this year or 2009. Now the plan is just to reintroduce Superman without regard to a Batman and Superman movie at all." With the financial and critical success of The Dark Knight, Robinov said that in the reboot Superman film, "We're going to try to go dark to the extent that the character allows it." Legendary Pictures president Thomas Tull said "Superman needs a powerful antagonist, a worthy opponent." Tull also wants to evoke Superman as an "angry God."