Above the Earth, a meteor shower damages an alien spacecraft, which then falls down to the planet's surface. A giant humanoid alien emerges and makes its way towards New York. In the Fantastic Four's headquarters in the Baxter Building, Ben is helping Reed to install some heavy equipment when they are alerted to the alien's presence in the city by Herbie and Sue. Reed, Sue and Ben board the Fantasticar and find the alien threatening a city bridge, at the same time as the army, air force and navy mobilise themselves for an assault on the alien. Meanwhile, the alien has badly damaged the bridge, leaving it up to Ben and Reed to fix it while Sue follows the alien. It attacks the Fantasticar and captures Sue, forcing the planned air strike against the creature to be called off. Sue turns invisible and manages to escape from the alien, and Herbie informs the rest of the team that according to his analysis of the alien's thought patterns, any harm to the alien would place the whole planet in jeopardy. Sue turns the alien invisible so that the army has nothing to fire at and the Four return it to the crashed spaceship. The Four then have to protect the alien from the army and find out its secret.

Magneto travels to New York, seeking out the Fantastic Four. He uses his magnetic powers to break into the Baxter Building and challenges Reed for leadership of the team. Magneto battles Reed, and manages to defeat him, becoming the new leader of the Fantastic Four in the process. For the new team's first mission, Magneto claims that he has learnt that the City National Bank is about to be robbed, and after Reed insists that they follow Magneto's orders, the Four go to the bank and confound the robbers' plans by removing the money themselves for safekeeping. Magneto takes the money away himself to a secret location so the robbers will not be able to find it. After the rest of the team return to their base, Reed discovers proof that Magneto intends to keep all of the money for himself. He reveals that he only pretended to be defeated by Magneto in order to discover what he was up to. Now fully aware of Magneto's treachery, Reed once again commands the team into a battle with Magneto in order to discover what he was up to. Now fully aware of Magneto's treachery, Reed once again commands the team into a battle with Magneto in order to defeat him and return the money.

The Fantastic Four patrol the skies above New York in the Fantasticar when they spot a tank ramming into a bank and sucking out the money. They land and attempt to stop the tank from getting away, but find out that the tank was made of plastic and the whole event was a movie scene being filmed in the city. The movie's director, J.J. Collaso, is upset at the ruining of the scene for his movie masterpiece ""The Gigantic Vacuum Cleaner That Devoured New York"", and so Ben and Herbie volunteer to repair the props. Collaso then invites the Fantastic Four to star in an epic film to be called ""The Fantastic Four Battle The Flying Saucers From Outer Space"". With Collaso promising that their fees will go to charity, they agree to star in the film and go to Hollywood. At the studio, the team is unaware that the mysterious Phantom of Film City intends to ensure that the Four never leave the set. He has joined the movie by posing as its art director, Belmont. As the team begin filming, they are attacked by a giant robot prop designed by Belmont. They defeat the robot and go onto the next scene, which involves the Four boarding a flying saucer crewed by their old enemies, the Skrulls. The supposed prop takes off, and Belmont reveals himself to be a Skrull too, and together the Four have to stop their plans and return to the studio to finish their film.

Travelling over the Bavarian Alps in the Fantasticar to investigate reports of mysterious beings in the mountains, the Fantastic Four come under attack from Gorgon, an Inhuman. Their ship is forced down and they come into contact with the rest of the Inhumans, led by Medusa. She tells them that their hidden valley is known as the Great Refuge, and they have used their powers to keep it hidden from humanity for many years. She informs the Four that the Inhumans intend to reveal themselves to the human world and then rule it. The Four are imprisoned and Medusa uses a hypnotic ray on Ben, getting him to serve her. The rest of the team escape their cell, and Ben is ordered to capture Herbie. After Ben tracks Herbie down, the robot gets Ben to hit his head on the floor, restoring his memory. Reed and Sue retrieve the Fantasticar, and after avoiding attacks from a missile, Gorgon and Karnak, meet up with Herbie and Ben. However Crystal, another Inhuman, uses her power over the elements to ground the Fantasticar. Seemingly trapped by the Inhumans, the Fantastic Four have to find a way to stop the Inhumans' plans of conquest and free themselves.

Herbie is helping Ben exercise using Reed's testing room, when a mysterious lady enters their headquarters and is captured by the automatic defense systems. She introduces herself as Queen Sebel of Manopal and wishes to enlist the help of the Fantastic Four. She uses a hypnotic influence on Ben to get him to agree to the trip to Manopal along with the rest of the team. There she tells them of how the Great White Stone, a large and valuable diamond was stolen by bandits. While acknowledging a few problems with Sebel's story, such as why no one else was sent to look for the diamond, the Four agree to track it down for her by looking in the surrounding jungle. They soon come into contact with the bandits themselves, who tell the team that Sebel must be overthrown. Sue retrieves the diamond, but before she can study it, Ben and Reed, now both under Sebel's influence, insist that it must be returned to her, and leave Sue and Herbie with the bandits. She asks them what they wanted with the diamond and they tell her that she used her powers along with the diamond to enslave the people of Manopal. Sebel gets the diamond back and forces Reed, Ben and Herbie to work as slaves, and transforms Sue into diamond. Forced to work in the mines, the remaining three of the team find Miel, Sebel's sister, who was imprisoned over a thousand years ago. Reed and the rest of the team, along with Miel, are left to figure out a way of freeing both Sue and the people of Manopal from Sebel's powers.