The Fantastic Four recall the origin of their powers and their first battle with the Puppet Master during a Dick Clark charity show.
The Puppet Master turns the Thing against Fantastic Four, but his plans fall apart when his step-daughter, Alicia, falls in love with the Thing and sides with the team.
Namor, the Sub Mariner, rises from Atlantis onto dry land. He encounters Sue and kidnaps her, wanting her to be queen of Atlantis.
The Skrulls, a race of green skinned shape shifters, come to Earth and impersonate the Fantastic Four. They attempt to discredit them, hoping to keep them from interfering in their plans to conquer Earth.
The enigmatic Watcher warns the Fantastic Four of the impending arrival of the herald of Galactus, the Silver Surfer. They learn if he summons his master, all of Earth will be devoured.
As Galactus' plans unfold, the Fantastic Four try to reason with him, but it proves futile. The only way to defeat Galactus now, puts Johnny's life in mortal danger. Meanwhile, the Silver Surfer sees Alicia and his loyalties begin to change.
The Skrulls let loose a new danger for the Fantastic Four to face, a being that possesses their combined powers: Super Skrull! Will the team be able to take this villain down?
Doctor Doom has captured the Fanastic Four, taking them to his treacherous castle.
Sue learns about Doctor Doom's past, while the others deal with the castle's traps. When they find him, Doom offers a deal: travel back in time to retrieve an ancient casket or Sue will be killed.
Reed, Johnny, and Ben arrive in ancient Greece, with only forty-eight hours to find the casket. Their problems multiply, however, when they get into the middle of the Battle of Thermopalye.
The Fantastic Four are at a charity function at Rockefeller Center, when the building is dragged underground. It's discovered that the Mole Man is responsible and he plans for world domination.
A creature named Annihlus appears in Reed's lab, soon followed by his mortal enemy, Blaastar. The Fantastic Four learn these two enemies come from the Negative Zone and must return them before it's too late.
Doctor Doom steals the power of the Silver Surfer, becoming empowered with cosmic power. How can the Fantastic Four stop him now?
A nuclear explosion caused by Doctor Doom causes the Fantastic Four to lose their powers. Reed's efforts to restore their powers is cut short after Doom takes over the Baxter Building. The team will need the help of Daredevil to retake the Baxter Building and get their powers back.
The Frightful Four have arrived to destroy the Fantastic Four. They take control of Ben's mind to turn him against the team. Can the Fantastic Four overcome this threat? And who exactly is Medusa?
Gorgon is searching for Medusa to return her to the mysterious Great Refuge. Johnny is forced to help her, but Gorgon captures her. The Fantastic Four discover his hideout and find the Inhumans.
The Inhumans teleport back to the Great Refuge, but Johnny is teleported there too after jumping in after Crystal. The rest of the team try to find him, while it is learned Black Bolt's evil brother, Maximus, has taken over.
Reed discovers a strange ""goop"" that can affect people's emotions. It comes from the Micro Verse and Psycho Man wants it back. He captures Sue, making her into Malice, Mistress of Hate.
Natural disasters are raging on across Earth. The Fantastic Four head off into space, finding Thor and the source of the problems, Ego. The Fantastic Four and Thor can't stop them on their own and will have to rely on one person: Galactus.
The Black Panther attacks and lures the Fantastic Four to Africa. They find the Black Panther is leader of an African tribe and that they are under attack by the master of sound, Klaw.
Depressed over Crystal, Johnny meets a girl named Frankie Raye, who possesses the same powers as he does. Meanwhile, Terrax attacks Manhattan and demands the Fantastic Four fight Galactus. The team learns from Galactus that Terrax betrayed and poisoned him. The poison takes it toll and Galactus will have to feed on Earth.
Bruce Banner is in town, which means the Incredible Hulk is too. When the Hulk goes on a rampage, Ben gets in his way.
Sue needs life saving surgery and only her father can perform the operation, but he has been in hiding for years since being accused of murder. When he comes to help, he gets arrested after the operation. Meanwhile, the Skrulls release Super Skrull, who takes Franklin Storm's place to exact revenge.
The Impossible Man is on the run from Super Skrull. Johnny agrees to protect him if he tells Lockjaw to teleport him to the Great Refuge to see Crystal.
Sue insists the team get some R&R, but Johnny stays at home. The others head to Tee Vu island, which is home to a Kree Sentry. Meanwhile, Black Bolt destroys the negative barrier and frees the Inhumans, reuniting Johnny and Crystal.
Doctor Doom once again makes himself all-powerful by draining the Silver Surfer's powers. Do the Fantastic Four have any hope of defeating him this time?
