The film begins two years after the first, with Doctor Doom having spent two years trapped in a casket until being awakened by the Silver Surfer, promptly taking over Latveria once free. Doom desires to take the Surfer's powers, having been reverted to his organic form after provoking and being attacked by the Silver Surfer.
During Reed and Sue's wedding, the Silver Surfer attacks the beacon Reed had secretly built to track his movement, prolonging their wedding, again. The Human Torch tries to pursue the Surfer, but is caught and dragged into the upper atmosphere, where the Surfer lets him free fall. By coming into contact with the Surfer, Johnny's DNA is destabilized, allowing him to switch powers with his teammates though physical contact. Reed learns that the Surfer uses a cosmic energy similar to the energy gave the group their powers. He also finds out that a planet dies eight days after the Surfer arrives.
From Doom's encounter with the Surfer, they learn his board is his power source and take steps to separate him from it. While setting up devices to do that, Sue has a confrontation with the Surfer, in which he reveals he is not the destroyer, only its servant. Regardless, the Surfer is soon captured. The military proceeds to torture the Surfer for information. The Surfer tells Sue that his master is Galactus, an entity which must feed on life-bearing planets to survive, and that his board is a homing beacon for Galactus to follow.
Meanwhile, Doctor Doom betrays the military and steals the Surfer's board, gaining the Surfer's powers. Sue is stabbed by Doom in the ensuing conflict, killing her. As the Surfer is powerless to help, the Human Torch absorbs all three of his teammates' powers in order to become strong enough to defeat Doom and free the Surfer. The Thing manages to knock Doom into a lake after a battle between him and the Torch, where he is seen sinking, returning control of the board to its owner.
However, Galactus (portrayed as a massive cloud-like mass, somewhat akin to Gah Lak Tus) has already arrived. His power restored, the Surfer resurrects Sue and decides to defend his newfound friends by flying into Galactus. After managing to repel Galactus, the Surfer is shown floating in space along with his board. Elsewhere, Reed and Sue finally get married, though yet another interruption forces them to rush the ceremony.
After the first credits the Silver Surfer is revealed to still be alive.