Doctor Doom entraps the Baxter Building into a net. Reed Richards recall how his classmate rival got expelled for injuring himself and endangering others in the college with his experiments on dark magic. Getting Sue to surrender as hostage, Doom forces the others to travel back to the past with his Time Platform to retrieve Black Beard's chest which contains the Stones of Merlin. After they bring back an empty chest, the Fantastic Four manage to escape and Doctor Doom flies away from his blazing castle.
Doctor Doom finds the Sub-Mariner and offers him to join forces against the Fantastic Four and all mankind. After Namor has installed his magnetic grabber inside Baxter Building, he pulls the whole structure into space to get rid of the four heroes and of Namor, who might pose a threat to his world domination plans. But the betrayed Atlantean has teamed up with the Fantastic Four and boards his spaceship, so Doctor Doom is forced to escape and ends up adrift, clinging to a speeding meteor.
After drifting in space and getting rescued by the a very advanced race of aliens called the Ovoids, Doctor Doom is taught their secret on how they are able to exchange bodies. Back on Earth, Doom captures Mt. Fantastic and switches bodies with him. He puts in motion a scheme to submit the Fantastic Four to a reducing ray, but his selfishness blows his cover. Shocked of being exposed, he lowers his guard and he and Richards resume their own bodies. The villain accidentally activates the reducing machine and gets caught in its ray, causing him to shrink to nothingness.
After being exposed to his own shrinking ray, Doctor Doom discovered the peaceful Micro-World. He gained the trust of the King and his daughter Princess Pearla, but he soon created another shrinking ray that enabled him to take over their world. Then he built a device to lure the Fantastic Four into the Micro-World, and after they have arrived, he contacted the Lizard Men of Tok to make an alliance with them in exchange for delivering them the heroes as slaves. After the Fantastic Four have managed to escape their cell and used his ray to grow back to his size, the Thing sends the Lizard Men back to Tok. Doctor Doom decides to resume his normal size and flee to his own world where he kidnaps Alicia and threatens to terrorize the city with his evil inventions if the Fantastic Four oppose him. The heroes find him in his floating laboratory but Doom chooses to escape by jumping off his hideout.
Doctor Doom recalls how he used his flying belt to safely land after jumping off his floating lab to escape the Fantastic Four. He decides to convince Spider-Man to team-up with him to defeat the quartet but the young hero refuses. Doom decides to capture him and use him as a bait to force the Fantastic Four to surrender. His instruments locate Peter with success, but the villain unknowingly kidnaps another boy nearby who has dressed up as Spider-Man. He realizes he abducted the wrong man when the real Spider-Man shows up and engages in battle. Spider-Man proves he is a strong opponent, and when the Fantastic Four arrive on the scene, Doom understands he stands no chance and escapes again.
While visiting his mother's grave, Doctor Doom remembers his tragic past. When Victor von Doom was but a child living among the gypsies, his father died after an attempt to flee execution by the Baron for failing to heal the Baroness. His son was left in the care of their servant Boris, who feared that Victor would follow the dark path of his late mother who was a sorceress. The boy grew up to be a handsome but cunning young man and his genius earned him a scholarship at an American university where he first met Reed Richards. The reclusive von Doom began experiments to contact the netherworld but got expelled after an explosion disfigured him. Travelling to Tibet, he was welcome by a group of monks who taught him all their secrets on black magic. After forging himself an armored suit and a mask, Victor flew back to his homeland as Doctor Doom where he now stands monarch of Latveria.
Doctor Doom bails three criminals out of jail and gives each of them super-powers suited to their basic traits. All three successfully capture the Fantastic Four but Doom rewards them by sending to another dimension. The prisoners break out of their cages and Doctor Doom ends up falling through spatial breach.
Adrift in space, Doctor Doom was picked up by Rama-Tut. Sharing the same hatred for the Fantastic Four, they realize that they could be the same man from different times. Rama-Tut sends him back to Earth while he returns to the 25th century. Doctor Doom orders a reception at the Latverian Embassy where he drugs the Fantastic Four so they fight each other. But Reed Richards returns the favor and gives Doom the illusion that he vanquished his rival in a mental duel. With no more interest in the Fantastic Four, Doctor Doom leaves.
While he attends a hypnotist act, Dr. Doom's mental veil is dissolves and the villain realizes that Reed Richards has tricked him. Taking over the Fantastic Four's headquarters, he soon finds out that they have lost their powers and uses Richards' own inventions against the team. But thanks to Daredevil, the heroes have time to get their powers back. Doctor Doom is defeated by the Thing who crushes his hands and destroys his armor.
Doctor Doom vows to get revenge on the Thing who seriously injured his hands during their last encounter and intends to use an Emotion Changer to destroy the Fantastic Four.
To get revenge on the Fantastic Four, Doctor Doom activates his Emotion Charger which fuels the hatred of all their enemies and causes an army of super-villains to assault Baxter Building on Reed and Sue's wedding day. But while the battle rages on, Reed uses a machine that transports all their enemies back to the recent past with no memory of what occurred.
To put fear in the Fantastic Four's heart, Doctor Doom plans to defeat the Avengers. Then he muses on the possibility of himself being the same man as Kang and Pharaoh Rama-Tut in different centuries. Then he puts ins plan in motion and sets a trap for the Avengers by sending a letter to the Scarlet Witch and Quicksilver announcing that they have family in Latveria. Once they have arrived, Doom seals the land within a giant dome. Despite the citizens' plea to lift the dome so a child can get a medical treatment, the despot refuses to comply. But the Avengers' joint effort enables the heroes to deactivate it and escape.
