An earthquake rocks New York, and Johnny spots that the whole city block has disappeared into the Earth's surface. Reed quickly deduces that this was the work of the Mole Man. The villain himself sinks Science Hall where Sue was giving a speech to a group of leading scientists, and tells the rest of the team not to interfere with his plans.

Reed has been elected to ask the villainous Professor Gamma to surrender himself and to destroy his Island X base in order to answer for his crimes against the world.

Ben is helping Reed to test out Sue's new force field, when they start receiving complaints from the Baxter Building's other tenants. Reed decides to take the team's tests to an isolated island. When the Four get to the island, the team is stranded there when their U-Car is stolen.

The Fantastic Four are lost in a Transylvanian forest while on vacation, and eventually come across an old castle. They are warned that the castle belongs to Diablo, an evil alchemist was was sealed away in the dungeon exactly 100 years ago.

Reed is exploring sub-space with his equipment while Johnny takes a vacation. Soon however, Klaws, the master of sound, arrives at the Baxter Building and attacks the remainder of the team with sonic booms.

Reed uses his time-space dimension machine to observe a strange distant planet in the midst of a giant battle. The planet's inhabitants are fighting Blast Starr, an incredibly powerful being capable of throwing power bolts from his hands.

A U.F.O. appears over the Earth, and after the air force attempt to intercept it, the craft's robot pilot abducts the Fantastic Four from an awards ceremony.

As the Fantastic Four answer the Yancy Street Gang's challenge to Ben, they quickly discover that it was a trap, and are attacked by three mutant apes.

Johnny is testing his ability to throw flares when he notices a strange object emerging from the sea. A blue-skinned woman emerges and introduces herself as Lady Dorma of Pacifica. She asks the Fantastic Four for help in fighting the tyrant Attuma, whom she inadvertently allowed to defeat the kingdom's rightful ruler, Prince Triton.

Ben is insulted by the Yancy Street Gang and becomes depressed over his appearance. The rest of the team visit an Egyptian museum and find an ancient tablet apparently depicting Ben returning to his human form. Reed tells him about the tablet, and the Four travel to Dr. Doom's castle to use time machine to travel back to 10th Century B.C. Egypt.

An alien ship from deep space approaches Earth and abducts the Fantastic Four. The robotic crew take the super-team to their world, where Reed is informed that he and the rest of the Four are being charged with crimes against evil, with the team's accusers being Klaws, Molecule Man, and Blast Starr.

Dr. Doom heads towards New York, claiming diplomatic immunity. Sue and the police commissioner summon all the team members to the Baxter Building, where the Fantastic Four prepare for Doom's arrival. There, they get a message from Doom, who tells Reed that he should say goodbye to his team-mates as he only has a few hours left to live.

On the Skrull homeworld, the Skrull emperor attempts to destroy the Fantastic Four, but Sue protects them with her invisible shield. Marshall Drom then shows the emperor a new weapon that will not fail: the Super Skrull, who has all the powers of the Fantastic Four.

On the Skrull homeworld, Warlord Morat is out hunting game when he decides to capture the Fantastic Four in order to impress Princess Anelle's father, the emperor of the Skrulls.

Reed experiments on a meteor for use as a new super fuel, an idea he got from a scientist named Professor Ivan Kragoff, a.k.a. The Red Ghost, and so the Four endeavour to use the fuel to get to the Moon, winning the space race before Kragoff, and to explore a mysterious blue area on the Moon's surface.

The villainous Impostor poses as the famous director Otto von Lenz after kidnapping the genuine article. He invites the Fantastic Four to star in a film of their own, and they readily accept his offer.

Dr. Doom appears on the Fantastic Four's TV, and challenges them to a duel to the finish. He predicts that he will remove the heart of the team, remove the team's greatest strength and finally, that the strongest power will conquer all.

Another Sun suddenly appears in the sky, which soon disappears and gives way to millions of floating rocks in the sky. A being known as the Watcher appears to the team and tells them that he caused the illusions, trying to hide the Earth from the Silver Surfer, a being who serves Galactus, who drains planets of their energy.

Whilst Ben is delivering a piano across town, he starts shrinking until only a couple of inches tall. The same thing happens to Sue while out shopping, Reed while testing a new aircraft and Johnny while fixing his car.

A meteor from deep space lands on a remote farm, and after Reed studies it back at the Baxter Building, he discovers that it has energy-absorbing properties.