For five years, Superman (Brandon Routh) has abandoned his adopted home of Earth while on a journey to visit the remains of Krypton. His seemingly selfish decision has ruined his image in the eyes of many, including journalist Lois Lane (Kate Bosworth), who writes a scathing article claiming that the world "doesn't need Superman". Scientist Lex Luthor (Kevin Spacey), who lost his fame and fortune after being exposed as a criminal by Superman, secures an early release from prison and marries an old heiress, whose subsequent death makes him wealthy once again. Upon returning to Metropolis, Superman, in his human identity of Clark Kent, is shocked to discover the consequences of his disappearance. While covering the launch of a space shuttle, he narrowly saves a plane carrying Lois and other observers from crashing after a mysterious power failure, an act that earns him much goodwill. Unbeknownst to anyone, the accident was triggered by Luthor using Kryptonian technology stolen from the Fortress of Solitude.

Clark tries to fix his relationship with Lois, but soon learns that she is engaged to Richard White (James Marsden), nephew of Daily Planet editor-in-chief Perry White (Frank Langella), with whom she shares a young, asthmatic son, Jason (Tristan Lake Leabu). Luthor has his aide Kitty (Parker Posey) distract Superman, allowing Lex to steal a sample of kryptonite from a museum. Suspecting his involvement, Lois requests an off-the-record interview aboard his private yacht. Luthor admits that he is indeed responsible and reveals his true plan: to create a new continent modeled after Krypton that he can shape in his image, while triggering massive tsunamis that will wipe out the nations of the world and force humanity to turn to him for survival. Jason has an asthmatic attack when Luthor reveals the kryptonite, but has no subsequent reaction when Luthor holds the stone near him.

Jason is sitting by the piano and the Yacht starts to rock from the waves. As the floor tilts, the piano is next seen skidding across the room, from off-screen, and crashing into one of Luthor's henchmen when he threatens Lois. Luthor and his thugs escape by helicopter as the new landmass emerges from the ocean. While working to contain the damage to Metropolis, Superman learns from Richard that Lois is in danger and saves her and Jason seconds before the yacht sinks.

Superman tries to apprehend Luthor, but the kryptonite-poisoned atmosphere quickly strips him of his powers. After letting his men beat him into submission, Luthor stabs Superman with a Kryptonite shard and leaves him to die. With Richard's help, Lois gets him to safety and removes the shard. Fueled by the sun's radiation, Superman defeats Luthor's gang and covers the landmass with soil, allowing him to safely throw it into space. While helping Luthor escape, a disillusioned Kitty allows the helicopter to crash on a remote island, trapping him. Complications from Kryptonite exposure cause Superman to fall into a coma, and while doctors are able to remove most of the fragments, they cannot revive him. Lois visits him and whispers something into his ear while glancing at Jason, after which Superman comes to. Acknowledging that he has a much greater responsibility than himself, he recalls 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 into space, where he gazes down at the world.

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