For five years, Superman (Brandon Routh) has been absent from Earth, lured into the depths of space by the hope that the lost planet Krypton may still exist. In his absence, much has changed on Earth; terrorism has surged, and Lois Lane (Kate Bosworth) has settled into a new life with Perry White's nephew, starting a family and earning a Pulitzer Prize for her article, "Why the World Doesn't Need Superman." Meanwhile, the cunning Lex Luthor (Kevin Spacey) has deceived a wealthy widow, Gertrude Vanderworth (Noel Neill), out of her fortune, assuming he has turned over a new leaf after his prison stint.
After inheriting her wealth, Lex, alongside his assistant Kitty Kowalski (Parker Posey) and a few henchmen, commandeers Gertrude's luxury yacht to venture northward, aiming for Superman's Fortress of Solitude. Once there, Lex discovers several crystals within the fortress's control panel, which contain valuable information from Superman's father, Jor-El (Marlon Brando). After hearing the holographic message, Lex returns to Metropolis with the crystals in hand.
Back on Earth, Superman lands near the Kent Farm in Kansas, where he reunites with his mother, Martha Kent (Eva Marie Saint). After reconnecting, he adopts his Clark Kent persona once more and makes his way to Metropolis, where he's welcomed by reporter Jimmy Olsen (Sam Huntington) and Perry White (Frank Langella). However, his long-awaited reunion with Lois is interrupted when she's aboard a jetliner set for a shuttle launch. An unfortunate mishap occurs when the shuttle fails to disengage, igniting the jetliner’s engines and jeopardizing everyone on board.
Acting swiftly, Superman springs into action, managing to separate the shuttle from the jet, but the plane begins to nosedive towards a packed baseball stadium. With his remarkable speed, he saves the jet from disaster just in time, eliciting cheers from the crowd. However, unbeknownst to him, the shuttle's malfunction was orchestrated by Lex, who set off a power outage to aid in his schemes.
As Lois investigates the blackout, Perry directs the Daily Planet staff to cover Superman's return instead. Clark confronts Lois and learns about her fiancé, Richard White (James Marsden), and their son, Jason (Tristan Lake Leabu). Their encounter leads to a poignant moment atop a building, where Lois expresses bitterness over Superman's absence, yet he remains resolute in his belief that the world still needs him.
Determined to move past the emotional turmoil that ties him to Lois, Superman resumes his call to justice. During this time, he unexpectedly saves Kitty from a car accident, not realizing it’s a trap designed to distract him. Meanwhile, Lex prepares for a heist at the Metropolis Museum, aiming to acquire the Addis Ababa meteorite, which contains kryptonite.
As Lois delves deeper into the mysterious power outage, she finds herself in a perilous situation aboard Lex's yacht. There, he reveals his grand scheme: to use the crystals to raise new continents, effectively flooding much of the current landmasses and profiting from the chaos. Lex’s heartless plan comes to light when he exhibits the kryptonite he possesses, which could spell doom for Superman.
In a stroke of fate, Lois’s son Jason displays hidden powers, protecting her from danger. After a series of intense confrontations, Superman is ultimately caught off guard by Lex and subjected to a vicious attack, weakening him. However, Lois, Richard, and Jason rally to save him just in time. With a renewed sense of purpose, Superman absorbs energy from the Earth’s sun before confronting Lex again.
In a colossal showdown, Superman challenges Lex on the newly formed continent, fraught with kryptonite. Overwhelmed, he endures devastating blows but pushes through his pain to thwart Lex's ambitions. After an arduous battle, Superman collapses, and the world faces the grim possibility of losing its savior.
While the city mourns, with hope dwindling, Lois and Jason share a final moment with him at the hospital. In a touching scene, Lois whispers words of encouragement into his ear, instilling faith that he will rise again. As they leave, Jason hugs Superman's costume, hinting at his unique lineage.
In a powerful denouement, Superman asserts his promise to Lois as he silently observes her and their son one last time. He takes to the skies once more, fulfilling his role as the protector of Earth, reaffirming, as he flies away, that he will always be there when the world calls for him.
