Superman (Brandon Routh) has been missing for five years, since traveling to the location where astronomers believed they had discovered the remains of Krypton. During his absence, Superman’s nemesis, mad scientist Lex Luthor (Kevin Spacey) was released from prison (due to Superman’s failure to appear at Lex’s trial) and married a rich widow (Noel Neill) to obtain her fortune upon her death. Superman, having failed in his quest to find surviving Kryptonians, returns to Earth and, as Clark Kent, resumes his job at the Daily Planet in Metropolis. He subsequently learns that Lois Lane (Kate Bosworth) has won the Pulitzer Prize for her article “Why the World Doesn’t Need Superman.” Meanwhile, Lex travels to the Fortress of Solitude and steals Kryptonian crystals, to use for an experiment that causes a mass power outage on the East Coast. The power loss interferes with the flight test of a space shuttle to be launched into space from its piggy-back mounting on an airliner, occupied by Lois Lane, who is covering the story. Clark flies into action as Superman and stops the plane from crashing onto a baseball stadium.
The world rejoices at Superman’s return, but he has difficulty coping with Lois’ fiancé, Richard White (James Marsden), nephew of Daily Planet editor-in-chief Perry White (Frank Langella), and her 5-year-old son, Jason (Tristan Lake Leabu). With Superman distracted by an out-of-control vehicle, a diversion involving Lex’s partner-in-crime, Kitty Kowalski (Parker Posey), Lex steals kryptonite from the Metropolis Museum of Natural History. Perry then assigns Lois to interview Superman while Clark investigates the blackout. Lois and Jason inadvertently board Lex’s yacht and are captured after Lois decides to investigate the blackout story, which she connects to Luthor’s experiment. He reveals to them his latest scheme to grab land and power. By combining one of the stolen Kryptonian crystals with Kryptonite, Luthor can grow a new continental landmass in the Northern Atlantic Ocean, one that will cause sea levels to rise drastically, killing billions of people and affording him full control of the only available land for the survivors.
Noticing Jason experience a slight reaction to Kryptonite, Lex asks who Jason’s father really is; Lois asserts that the father is Richard. The crystal begins to create Lex’s new landmass, while Lois attempts to escape but is attacked by a henchman. Jason throws a piano at the henchman, killing him and proving that he is actually Superman’s son. 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 from the sinking yacht. Superman soon arrives to help and then flies off to find Lex.
Meeting Lex, Superman discovers the landmass is filled with Kryptonite, which weakens him to the point that Lex and his henchmen are able to beat him. Superman is stabbed by Lex 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 after putting layers of earth between him and the Kryptonite. Lex 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 tiny desert island when their helicopter runs out of fuel. Superman pushes the landmass into space with the crystals trapped on the landmass, but is weakened by the Kryptonite and crashes back to Earth. At the hospital, doctors remove more Kryptonite from Superman’s wound, but their surgical tools and hospital machines are either damaged or destroyed when they try to revive him. While Superman remains in a coma, Lois and Jason visit him at the hospital where Lois whispers something into Superman’s ear and then kisses him. Superman later awakens and flies to visit Jason, reciting his father Jor-El’s (Marlon Brando) 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.