This issue opens on Mr. Fantastic using an electronic x-ray camera to take photos of the Invisible Girl in the hopes of finding out the way in which she turns invisible. As he's studying the photo, the Fantastic Four's emergency flare shoots outside the window, and he figures that it must be the Thing, as he's the only member of the Fantastic Four not at the Baxter Building at that time. Mr. Fantastic, the Invisible Girl, and Human Torch all leave the Baxter Building, and head for where the flare came from, whilst avoiding their fans, who all want autographs. When they reach the Thing, it turns out to be a false alarm, as the Thing says that he only called them there to show them some of Alicia Master's sculptures of enemies they've encountered in the past. All of the Fantastic Four agree that the sculptures are realistic, but Sue asks why Namor was included, as he isn't as bad as the rest of their enemies.
Mr. Fantastic then starts to talk to Sue about the Sub-Mariner, before the scene cuts to Stan Lee and Jack Kirby's studio, where they're planning the villain of the current Fantastic Four issue. As Stan Lee mentions that it's a pity Doctor Doom was lost in space, as he was a brilliant villain, Doctor Doom himself steps into the room. The creators ask Doom how he managed to return from space, but Doom says that it's a long story. He then makes Lee and Kirby call Mr. Fantastic to the office and discuss a new plot, and then when Mr. Fantastic arrives, Doom uses a sleeping gas to knock him out. Doom then gives Lee and Kirby a card with his address on it, and tells them to tell the rest of the Fantastic Four to meet him there, before teleporting out. When Mr. Fantastic awakes, Doom explains that when he was last seen, he was being carried out to space on a meteor (in Fantastic Four #6). The meteor soon reached a space ship where a race called the Ovoids lived, who had science years ahead of Earth's. Doom managed to steal some of their secrets from them before being taken back to Earth by them.
As Mr. Fantastic tells Doom that he's mad, Doctor Doom explains that one of the Ovoid's powers is the ability to transfer their minds to another body, and whilst he was talking, he was slowly using that power on Reed. As he finishes saying this, Doctor Doom's mind fully changes to the body of Reed Richards, and vice versa. Mr. Fantastic tries to stop him, but as Doom has Reed's elasticity, he is easily able to hold him off long enough for the Fantastic Four to arrive, who naturally don't believe that Doom and Reed have swapped bodies. The Fantastic Four then lock Mr. Fantastic (still in Doom's body) in a gigantic glass prison, which has two oxygen canisters in it.
Back at the Baxter Building, Doom (still in Mr. Fantastic's body) reveals that he is creating a shrinking ray. Although the other members of the Fantastic Four are suspicious of why he is doing it, Doom manages to convince them that by shrinking them and then enlarging their size back to normal, their powers will be increased. All of the Fantastic Four are excited by this, but after they've gone, Doctor Doom thinks to himself that if he can get them in front of his shrinking ray, then he can shrink them down to nothingness. Meanwhile, back at his prison, Mr. Fantastic manages to escape from his glass prison by throwing the two oxygen cylinders into each other, creating an explosion which destroys the glass. Mr. Fantastic then goes to Alicia Masters for help, but the Fantastic Four are there at the same time as he is, and are all going to attack him. However, they find that they instinctly can't hurt Reed, and head back to the Baxter Building to decide what to do with him.
When Mr. Fantastic is taken into the building, Doctor Doom decides to shrink down the Fantastic Four to nothingness whilst Reed is helpless, so that he can then dispose of him at his leisure. However, Reed once more tries to interfere and save them, and Johnny starts to think that maybe Mr. Fantastic and Doctor Doom did swap bodies. He then creates a heat mirage of dynamite, and whilst Reed tries to defuse the dynamite, Doom tries to escape. The Fantastic Four get Doom back and then believe that they did swap bodies, which shocks Doom so much that returns to his original body, and Reed to his. Whilst Doctor Doom tries to stop the Fantastic Four, he accidentally falls in front of the shrinking ray, and is shrunk down to nothingness before anything can be done to save him.