

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.
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.