For five years, Superman (Brandon Routh
) has been away from Earth, coaxed into space by a belief that Krypton may still exist. In the time he's been away, the world has changed--not only has terrorism become rampant, but Lois Lane has been living with Perry White's nephew, started a family, and won a Pulitzer Prize for her piece "Why the World Doesn't Need Superman."
Also during this time, Lex Luthor (Kevin Spacey
) has conned a wealthy widow named Gertrude Vanderworth (Noel Neill
) out of her fortune, with the assumption that he has changed his ways after being in prison. After inheriting her money, Lex, his assistant Kitty Kowalski (Parker Posey
), and some henchmen take Gertrude's private yacht, and head North toward Superman's Fortress of Solitude. Lex carefully guides them to the location, where he finds several crystals, and the holographic image of Superman's father, Jor-El (Marlon Brando
). After listening to the hologram, Lex and his crew take the crystals and return to Metropolis.
Meanwhile, Superman returns to Earth, landing near the Kent Farm in Kansas where his mother, Martha Kent (Eva Marie Saint
), currently resides. After spending some time with her, Superman re-adopts his Clark Kent persona, and returns to Metropolis. Reporter Jimmy Olsen (Sam Huntington
) and Daily Planet Editor Perry White (Frank Langella
) are there to greet Clark. However, his reunion with Lois Lane (Kate Bosworth
) is put on hold, as she is aboard a jetliner being used to launch a new shuttle into space. However, the shuttle fails to disengage before it's engines fire and rocket the jetliner in orbit, the flames from the shuttle's engines burning the plane's tail section.
Superman flies into action, and manages to disengage the shuttle, but the jet ends up plummeting to Earth, with it's tail section burned up. Chasing it into the Earth's atmosphere, Superman manages to stop the jet before it crashes into a baseball stadium filled with people as a game is underway. After greeting the press and the public in the cheering stands, Superman takes off.
Unknown to Superman and the rest of the public, the shuttle's error was due to a brief power outage that affected much of the country. This was caused by Lex Luthor, who, after taking a sliver from a crystal, placed it into some water in a model train layout in the basement of Gertrude Vanderworth's mansion. This triggered an EMP (electromagnetic pulse) reaction that cut off local power, but resulted in a large crystal growth to blossom from the sliver, that ends up demolishing the model, and growing up through the basement.
Back at the Daily Planet, Lois wants to find out more about the power outage, but Perry White wants the entire staff to focus on getting as much information on Superman as possible. It is during this time that Clark reintroduces himself to Lois, and meets her long-term fiance Richard White (James Marsden
), and their child, Jason (Tristan Lake Leabu
). After their encounter, Superman later meets Lois on the roof, where they have a heart-to-heart talk, and Lois explains to him that she has moved on.
Trying to distance himself from his emotions over Lois, Superman returns to fighting crime, not just in Metropolis, but all over the world. In one instance, he rescues Kitty Kowalski when the brakes fail on her Ford Mustang. However, this was all a ruse to keep Superman occupied, as Lex and some associates break into the Metropolis Museum to steal some Kryptonite. Shortly afterward, Superman returns to the Fortress of Solitude, where he finds the crystals containing the information regarding Krypton are now missing.
Lois continues to investigate the power outage, which leads her to the Vanderworth mansion, with her son in tow. Finding the mansion locked, she finds the Vanderworth yacht floating nearby, and goes aboard. Before she can react, the yacht has pulled away, and Lois finds herself face-to-face with Lex Luthor.
While aboard the yacht, Luthor begins to explain his plan to Lois. Using the crystals that he took from Superman's Fortress of Solitude, he intends to sink them into the ocean, creating brand new continents with enough land mass to overtake the Americas, Europe and Africa, and cause the oceans to rise, burying much of the present land mass, killing billions of people. With Luthor having a monopoly on land, he intends to charge exorbitant prices for people to live on his new continents.
Lex then leaves Lois and her son under the watchful eye of one of his henchmen before going to the main deck of the ship. One of the crystals is inserted inside a tube made of Kryptonite and placed inside a stolen Russian missile. As it is fired into the ocean, it creates a reaction that starts the growth of a new landmass, albeit riddled with Kryptonite.
Lois tries to distract their captor, and attempts to send a fax with their coordinates to the Daily Planet, but not before she's found out. However, before their captor can kill her, a piano flies across the room, crushing him. It appears to have been thrown by Lois' son...who it appears was actually fathered by Superman. When Lex hears of this, he has Lois and her son locked in the ship's pantry before the rest of them take off in a helicopter on deck to the newly-grown continent.
Back at the Daily Planet, the fax has partially come through, and Richard heads off to find Lois. Superman attempts to follow, but becomes side-tracked when the newly-growing landmass causes a tremor that threatens the entire city. Superman has his hands full, saving people and averting catastrophes. Once it seems the tremors have stopped, he heads back out to sea. At the exact coordinates, he finds Richard's seaplane, but also the Vanderworth Yacht, skewered by a spiky growth from the new continent. Superman rescues Richard, Lois and Jason, before the Yacht cleaves in two, and disappears below the water.
As the family takes off, Superman heads to the 'New Krypton' continent to confront Luthor. Luthor greets Superman, who, with the environment teeming with Kryptonite, has grown weaker. Luthor and his thugs beat and pummel Superman, before Luthor stabs him with a Kryptonite shard, and sends him plummeting off a cliff to the waters below.
Superman is saved when Lois convinces Richard to go back, telling him of how the new continent is laced with Kryptonite. After Jason spots Superman in the ocean, Lois dives in and manages to catch hold of Superman's cape and haul him to the surface, while Richard gets him aboard the plane. Lois pulls out the Kryptonite shard, but is unable to remove it all. Regaining consciousness, Superman thanks them for the rescue, but decides to go back to stop Lex. Superman first breaks through the clouds above, to absorb as much energy as he can from the Earth's sun. Flying down, he burrows below the new landmass and then lifts it out of the water, shielding himself from the kryptonite underneath with as much rock and soil as he can.
Lex, Kitty and their henchmen attempt to flee the ascending continent, but all the henchmen are crushed by a massive chunk of falling edifice. Lex, Kitty and her dog manage to board the helicopter. Kitty, who is tinged with guilt about the how many are going to die if the other continents get created, throws out the other crystals. With no time to retrieve them, Lex pilots the helicopter away. Superman, growing weaker and weaker due to the Kryptonite-laced continent, manages to push it into space before plummeting to Earth, crashing into a park in Metropolis.
Superman is rushed to a hospital, where the remaining Kryptonite shard is removed, and the doctors attempt to revive him (spoiling several pieces of medical equipment in the process as they try to resuscitate him). However, after several days, he has not regained consciousness. A vigil is held outside the hospital by hundreds of people, and even Martha Kent is among them. Back at the Daily Planet, Perry White has two front pages ready to run: "Superman Is Dead" and "Superman Lives." Richard generously offers to drive Lois to the hospital, and Lois and Jason manage to get in and see Superman, though he does not wake. While Lois leans over the unconscious Superman, she whispers something softly in his ear, with a meaningful glance at Jason; we are led to think that she has told Superman that he has a son. Jason is entranced by Superman's costume lying on a chair, and as they leave, Jason dashes to Superman's bedside and gives him a brief kiss goodbye. As Lois and Jason are escorted from the hospital, Martha spots them, and gazes speculatively at Jason. We see Lex and Kitty stranded on a small desert island with no food or water. When Kitty wonders aloud what are they going to eat, Lex eyes Kitty's little dog that she's cradling. Shortly afterwards, as a nurse checks on the room, the bed is found to be empty, the window open, and the costume gone.
Later that evening, Superman flies to Lois and Richard's house. Lois is at her desk tearfully attempting to start writing another article: "Why The World Needs Superman." Superman slips into the house to gaze at Jason, who is asleep. Superman repeats the same words his father spoke to him so many years before: "You'll be different. Sometimes you'll feel like an outcast. But you'll never be alone. You'll make my strength your own. You'll see my life through your eyes, and your life will be seen through mine." Gently he caresses Jason's head, and finishes softly, "The son becomes the father, and the father becomes the son." Just before he leaves, Lois, who is outside, suddenly hears Jason piping, "Goodbye!" and sees Superman leaving. She asks him if they will see him again, and before he flies away, he assures her that he will always be around.