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.

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.

In Latveria, Doctor Doom plans to defeat the Fantastic Four before ruling the world himself. Doom travels to New York and ensnares the Baxter Building with a giant electrical wire. He reveals himself to the Fantastic Four, and Reed recognizes Doom. Reed tells the others of how he and Victor Von Doom were once classmates at college years ago and that Doom's forbidden experiments resulted in an explosion which scarred his face and resulted in his expulsion. Doom travelled the world in search of specialists to restore his face, but to no avail. He eventually ended up in Tibet and obtained many secrets of science and sorcery from a remote monastery, along with a suit of armor. Reed agrees to go to Latveria in order to face up to Doom's challenge, and the rest of the team go with him. In Doom's homeland, he tells the Four of how he needs more wealth in order to rule the world and gets Reed, Ben and Herbie to travel back in time to take the treasure of Blackbeard the pirate, while holding Sue hostage. Back in the past, the rest of the team dress up as pirates in order to be less conspicuous, and end up joining a pirate ship's crew. They search the ship and find the treasure in the captain's quarters. After defeating the crew, Ben is hailed as being the greatest of all pirates by the crew, who dub him Blackbeard. With the real identity of Blackbeard discovered, Reed has to figure out a way of keeping the treasure safe from Doom before they return to the future and to then rescue Sue.

In an isolated mansion deep in a far away forest, the super-villain known as the Wizard has invited Medusa, the Sandman and the Trapster. He tells them that they must work together as a team in order to defeat the Fantastic Four, and that they will be called the Frightful Four. Back at the Baxter Building, the Fantastic Four are alerted to a jewellery store robbery and leave to deal with it. Herbie detects the presence of the Wizard and his new team, and they carefully prepare to deal with this new menace. Reed and Sue deal with the Wizard and Medusa while Ben and Herbie are left to stop the Trapster and the Sandman. Not properly prepared to deal with the Frightful Four, the Fantastic Four are out of their depth and the Wizard's new team manages to escape from them. As the Fantastic Four have to deal with their very public defeat, the Frightful Four begin to argue among themselves before the Wizard tells them to follow his new plan. They lure the Fantastic Four to a bank, where they begin to fight among themselves as a result of one of the Wizard's spells. During the fracas, Medusa kidnaps Herbie. After the spell has worn off, the Wizard challenges the Fantastic Four to rescue their comrade from his mansion. At the Wizard's mansion, they have to survive the many traps and liberate their friend as well as ensuring that the Frightful Four are defeated for good.

Doctor Doom leaves Latveria for New York on his royal rocket. Herbie detects the rocket's launch and Doom makes his way to the Latverian embassy. There, he broadcasts a holographic message to the Fantastic Four. Doom tells them that unlike previous occasions, this time he will finally defeat the Four. Not wanting Doom to make the first move, the Four split up and search the city for Doom's whereabouts. Having no success, Reed suggest the team take time out to relax. Ben goes bowling, Reed attends a science convention, and Sue gets here hair done. At each of their chosen locations, the Four are constantly followed by bizarre Doom-balloons floating in the air. The balloons cause the Four to attract ridicule and disrespect from various members of the public, and so they return dejected to the Baxter Building. Doom again contacts the Four and tells them that they will never be able to stop him. Reed discovers that each of them was bugged by Doom, explaining how the balloons followed them. Meanwhile, after having his request for total command of the U.S. armed forces denied by the Pentagon, Doom cuts off the electrical power for the whole country. As the nation grinds to a halt, Reed and Herbie track down Doom's satellite-ship base, but as Doom's balloons were constantly recording the molecular structure of each of the Four, only Herbie with his interchangeable components can disarm Doom's alarm system. After doing so, the rest of the team are able to enter Doom's ship and contend with many booby traps. In the end it falls to a battle of wits between Reed and Doom to determine the victor.

Reed's new experiment yields in the discovery of another dimension known as the Negative Zone. He wants to see if the Zone contains new power sources to help the Earth's energy crisis. Sue then shows the team Lockjaw, the Inhumans' giant teleporting dog, who she borrowed from Medusa. With Lockjaw's help, Ben and Sue are able to teleport themselves to the Negative Zone to retrieve mineral samples. While in the Zone, they come under attack by winged creatures, but manage to defeat them. They soon discover a very large cocoon and realize that the creatures were trying to keep them away from it. Sue hears a heartbeat coming from the cocoon and Reed tells here to bring it back with them. Feeling tired and overworked, the Four decide to go out for dinner leaving Lockjaw to guard the cocoon. Feeling rejected, Lockjaw looks to the cocoon for company. Soon the cocoon bursts open, revealing the evil Blastaar, capable of firing enormous power bolts from his hands. Having overheard the Four talk of Lockjaw's teleporting abilities, he uses the dog to take him all over New York, destroying anything in his way. The team attempt to stop him, but with Lockjaw's help, Blastaar always gets away. The Fantastic Four are left with having to track Blastaar down and imprison him again.

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.

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.

With nothing to do on a quiet night, Ben takes the Fantasticar out for a spin and observes a spaceship in the sky. The spaceship abducts Ben, and the rest of the team attempt to track the ship down. The spaceship travels to the dark side of the Moon, and the commander of the ship, Sandro of the Centaurians, introduces himself to Ben. He tells him that they have been at war for a long time with the Polarians, and to end the war, each side has chosen a champion to fight for them. The Centaurians have chosen Ben to fight for their planet's supremacy and force him into the contest by threatening the Earth. Meanwhile, the rest of the team have tracked Ben down and hitch a lift on a Moon rocket. Inside an air-tight dome on the Moon, the Polarians led by Pollus arrive with their warrior, Monstro, a giant humanoid lizard. Monstro and Ben then compete with each other in a series of events, while Reed, Sue and Herbie enter the dome. Sue turns invisible and swaps the keys of the respective alien spaceships around. Ben and Monstro then work together and shatter the dome, causing the air to leak out. Trying to escape, the Centaurians and Polarians are unable to open their ships. Reed tells them that unless they develop a trust for each other and hand the proper keys back over, they will all run out of air.

On board a commercial airline, the Fantastic Four are travelling to Gateway University in St. Louis where Reed is due to receive and honorary degree when the plane is hit by a mysterious flying object. Together, the Four save the plane and then travel to the university. Reed meets with the dean, Johnson and tells him of what happened with their plane, and that he saw the object fly back to the university. Johnson suspects what has happened and shows Reed to his old teacher, Professor Gilbert's laboratory. There Gilbert shows his former student his latest creation, a giant winged android called Dragon Man. He reveals that Dragon Man's test flight was responsible for accidentally striking the plane earlier. With the help of his assistant, George, Professor Gilbert demonstrates how Dragon Man works by using a thought helmet to control the android. Resentful of not receiving what he thinks is his due, Gilbert's assistant George takes control of the Dragon Man, and disrupts Reed's ceremony. Gilbert tells Reed that the only thing Dragon Man is vulnerable to is extreme cold, and so the Fantastic Four formulate a plan to stop the Dragon Man once and for all.

A strange green rocket lands on Earth and turns into a powerful green alien. The first people he meets up with are a gangster named Grogan, and his accomplices who have just robbed a bank. The alien tells them that he is from the planet Popup on vacation and has no name. Since he can do just about anything, Grogan dubs him the Impossible Man. Taking advantage of his ignorance of Earth culture, Grogan plans to use Impossible Man to rob every bank in New York. The next day, they successfully steal a large amount of cash from a city bank. The Fantastic Four are alerted to the super-powered theft by the police, and track Impossible Man and his acquaintances to a local restaurant. Completely fooled by Grogan, the Impossible Man refuses to listen to the Fantastic Four's explanation as to what is really going on. Still not wanting to listen, the Impossible Man does battle with the Fantastic Four and manages to hold them off. Knowing that sooner or later the Four will have proof that Grogan is directly responsible for the resulting bank thefts, he has the Impossible Man go to the next bank on his own. At the bank, the Fantastic Four disguise themselves as bank workers and convince the Impossible Man to find out what Grogan really thinks about him. They have to hope that the Impossible Man listens to their advice and turns against Grogan, as well as figuring out a way of getting him off the Earth before he causes any more trouble.

In Europe, a large power plant sinks into the ground, the latest such occurrence. The Fantastic Four are contacted for help, and Reed mentions that a mysterious individual known as the Mole Man is the one who is apparently responsible for the power plants' disappearances. After feeding him the necessary data, Herbie predicts the next plant to disappear will be Russia's largest power plant. The Four travel to Russia and witness the power plant sinking into the Earth's surface. After other plants are sunk into the ground, Herbie tracks the Mole Man's base to the legendary Monster Isle, and the team sets out to find him. Experiencing bad weather conditions, the Four are forced to land on the island, with Ben and Herbie ending up in the Mole Man's lair. He tells them of how he was once a respected scientist who was convinced of the existence of Monster Isle and was ridiculed because of it. He eventually found the island and discovered strange mindless creatures that regarded him as their god. Having dwelt in the darkness for so long also made him develop a radar sense which he demonstrates by avoiding one of Ben's attacks. With Ben and Herbie helpless, the Mole Man tells them that he intends to make the world defenseless while his subterranean armies take over the surface. Reed and Sue track Ben and Herbie down, and together they must stop the Mole Man's armies and return all of the captured power plants to the surface.