Two years after the previous film, as Reed Richards and Sue Storm prepare for their fourth wedding attempt, a mysterious, silver phenomenon streaks into Earth's atmosphere from outer space, radiating cosmic energy that creates massive molecular fluctuations in specific locations across the Earth. The government approaches Reed to build a sensor to track the movements of the phenomenon, and he secretly complies, hiding the fact that he has taken the contract from Sue to stop her from worrying.
The wedding begins, but in the midst of the ceremony, Reed's sensor detects the phenomenon approaching New York, causing a massive power blackout across the city. The silver streak destroys the sensor while the Fantastic Four protect the crowd from a helicopter that has fallen from the sky, and the Human Torch then pursues it across the city. Catching up to it, he discovers that it is a silver humanoid riding a "surfboard" of liquid metal, and is then promptly seized by this "Silver Surfer" and dragged into the upper atmosphere. As his flame snuffs out, the Surfer drops him into free fall, but he manages to reactivate his powers enough to survive the fall. An examination by Reed discovers that Johnny's exposure to the Surfer has caused his DNA to become destabilized, allowing him to switch powers with his teammates through physical contact. Tracing the energy of the Surfer - a cosmic energy similar to that which gave the team their powers - Reed discovers that the series of planets that the alien has visited have all been utterly destroyed.
The Surfer's circuit of the globe has restored an old enemy to life - Doctor Doom, having spent two years paralyzed as a metal statue, has been returned to life, albeit hideously scarred. He traces the Surfer to the Arctic and makes him an offer to join forces, but when the Surfer rebuffs him, Doom attacks with an ineffective electrical blast. The Surfer returns fire, blasting Doom through the ice, but as an unexpected side-effect, the cosmic energy of the Surfer's blast heals Doom's body. Ever the schemer, he proceeds to offer his services and the knowledge he has acquired on the Surfer to the American military, who force the Fantastic Four to work with him. Deducing that the Surfer's board is the source of his power, the group develops a four-part energy-pulse generator that will separate him from his board, and track him to his current location. While setting up the pulse generator, Sue is confronted by the Surfer, in which he reveals he is not the destroyer of worlds, only its servant. Regardless, the military open fire on the Surfer, and while he is distracted, the pulse is fired and the board and Surfer are taken captive.
The military imprison the Surfer in a remote gulag, and forbid the Fantastic Four from interacting with him, while they torture him for information. Sue, however, uses her powers to invisibly sneak into his cell, where she coerces more information from the Surfer. He tells her his master was known by the people of his world as Galactus, an entity which must feed on life-bearing planets to survive, and that his board is a homing beacon for Galactus to follow, which even now summons him to the planet.
Meanwhile, Doom betrays the military, donning a suit of armor containing a device that allows him to take control of the Surfer's board, and gains the alien's cosmic powers. Realizing they must get the board off the planet, the Four free the Surfer from his cell and summon the Fantasticar to pursue Von Doom. When they encounter the thief, Doom refuses to cooperate and the Four are forced to battle him to confiscate the board. Eventually the destructive chase leads to Shanghai where Sue is impaled through the chest by Doom when she attempts to protect the Surfer by projecting a large force field around them both, eventually killing her. As the Surfer is powerless to help, Johnny absorbs all three of his teammates' powers in order to become strong enough to defeat Doom. When he destroys Doom's machinery and separates him from the board, returning it to the Surfer's control, Ben (powerless) manages to knock Doom into the harbor using a crane, where he is seen sinking. However, Galactus (portrayed as a massive cloud-like mass containing a burning core shaped like his helmet, somewhat akin to Gah Lak Tus) has already arrived. His power restored, the Surfer revives Sue and decides to defend his newfound friends by flying into Galactus and destroying him from the inside with a massive energy blast, apparently killing himself in the process.
Realising that they will always have to live in the spotlight because of who they are and what they do, Reed and Sue are married in a small ceremony, which is rushed through by yet another emergency alert that the team flies off to attend.
Seconds into the credits, the film cuts back to a shot of the Silver Surfer's seemingly lifeless body floating through space. Just as he drifts off the edge of the screen, his eyes snap open, and his board races out of shot to reunite with his body.
