As Reed Richards and Sue Storm prepare for their wedding, a silver object enters Earth's atmosphere, creating 1 mile wide craters across the Earth. General Hagar asks Reed to track and identify its movements. He initially refuses, to appease Sue, who feels he is again neglecting her for his work. However, he surreptitiously builds a radar tracker to locate the object, as the Army requests.
During the wedding, Reed's systems detect the phenomenon approaching New York City, which suffers a blackout since it emits electromagnetic pulses that cause power outages. Johnny Storm, the Human Torch, pursues the object, discovering it to be a silvery humanoid on a flying surfboard. The "Silver Surfer" drags him into the upper atmosphere, suffocating him, and drops him. During his fall, Johnny finds his flame powers fluctuating and barely survives, successfully flying only at the last moment. Later, Sue and Johnny switch powers when they touch, prompting Reed to deduce that exposure to the Surfer has affected Johnny's molecular structure, allowing him to switch powers with his teammates through physical contact. Tracing the cosmic energy of the Surfer, Reed discovers that a series of planets the alien has visited have all been destroyed.
With the Surfer creating craters around the globe, Reed determines that the next will appear in London. The team arrives too late to stop the crater, which drains the River Thames, but they prevent the London Eye from collapsing after it was damaged by the quake (though Johnny nearly thwarts their effect in the process when he switches powers with Reed). Afterward, Reed and Sue contemplate abandoning their lives as superheroes in order to have a normal life and raise a family, but are unaware that Johnny is listening. Meanwhile, the Surfer's movements around the globe bring him past Latveria, where the cosmic energy affects Victor von Doom, freeing him from two years encased in metal. Doom, able to move again but scarred, traces the Surfer to the Russell Glacier and offers to join forces. When the Surfer rebuffs him, Doom attacks. The Surfer retaliates, blasting Doom through the ice, but the cosmic energy of the Surfer's blast heals Doom's body.
Doom leverages his experience into a deal with the American military, who force the Fantastic Four to work with Doom. Deducing that the Surfer's board is the source of his power, Reed develops a tachyon pulse generator that will separate him from it, while Doom works on a machine whose function he keeps a secret. In the Black Forest, the Surfer confronts Sue and reveals he is merely a servant to the destroyer of worlds, and regrets the destruction he causes. The military opens fire on the Surfer, which distracts him and allows the Fantastic Four to fire the pulse, separating the Surfer from his board. The military imprisons the Surfer in Siberia, while they torture him for information. Sue uses her powers to sneak into his cell, where he reveals more information. He tells her his master, known by the people of his world as Galactus, is a massive one million mile long cloud-like cosmic entity that feeds on life-bearing planets to survive, and that his board is a homing beacon summoning Galactus to the planet. The Silver Surfer has to serve Galactus, who will otherwise destroy not only his loved ones but also his planet.
Doom, using the device he has created, betrays Hagar and steals the board from the compound using his device from earlier, killing the majority of the Army present there. The Fantastic Four rescue the Surfer and pursue Doom in the Fantasticar, confronting him in Shanghai. During the battle, Sue is mortally wounded. With the Surfer powerless, Johnny absorbs the combined powers of the entire team in order to battle the now cosmic energy-empowered Doom (also saying Ben's catchphrase). Johnny succeeds in breaking Doom's controlling device over the Surfer's board, and Ben Grimm uses a nearby crane to knock Doom into the harbor. However, Galactus has arrived, and Sue dies in Reed's arms. The Surfer regains control of his board, restoring his power. He revives Sue and chooses to defend Earth, flying, with an extra boost from Johnny, into Galactus. The conflict results in a massive blast of energy that engulfs Galactus in a cosmic rift, and apparently kills the Surfer as well. Johnny has recovered his stable molecular state after touching the Surfer's board.
Reed and Sue get married in Japan, in an abbreviated ceremony. Receiving news that Venice is sinking into the Adriatic, the team heads to Italy. In a post-credits scene, the Silver Surfer's seemingly lifeless body floats through space. His eyes then open and his board races toward him, showing that he is alive.