At the start of this issue, a red alert signal of the Fantastic Four's is sent out from the Baxter Building, causing the Human Torch, Thing, and Invisible Girl to go to the Baxter Building, even though it's inconvienient from all of them. To their surprise, when they reach the Baxter Building, there's no sign of an emergency, and Mr. Fantastic explains that he got a call from the chief of police saying that all of the mobsters and gang leaders in the country are heading to New York, and that something big is happening. Meanwhile, some of those gang leaders are meeting with a man who calls himself the Thinker, who claims that he can form a kingdom of crime with them, since he can use his intellect to predict what will happen, and avoid the police. Some of the gangsters point out that the Fantastic Four will be a hazard to the Thinker, but he adds that he hasn't forgotten about them, and that he never overlooks any detail.
The Thinker then explains how he was able to pull off some previous crimes thanks to predicting what would happen, but one of the gang leaders doesn't believe him. The Thinker says that in eighteen seconds he'll realise that the Thinker is right, and true to his word, the leader is captured by the police eighteen seconds later. The Thinker then explains how he'll get rid of the Fantastic Four: the Human Torch's cousin wants him to perform in his circus, Mr. Fantastic will be hired by an electronics company for their electrical research division, the Thing will join a wrestling competition, and the Invisible Girl will be hired by Hollywood. All of these things happen to the Fantastic Four, although they're reluctant to accept their offers, as they don't want to split up the team. When they all find out that they've been offered various things, the team agree to accept their offers, and split up, unknowingly doing what the Thinker wants them to do.
A meteor lands in the river near New York shortly afterwards, causing a blackout which allows the Thinker and his criminal comrades to go inside the Baxter Building whilst the defence mechanisms are off. The Thinker soon finds Mr. Fantastic's notes on DNA, and decides to create a new form of life to serve him. Shortly after this, the Fantastic Four all get bored with their new careers, and so return to New York at almost exactly the same time. When they reach their headquarters, they find that the Mad Thinker has taken over it, and has set up traps to delay their progress to the top floor. Despite these traps, the Fantastic Four manage to make it to the top floor, where they find the Thinker's android, which he created using Mr. Fantastic's notes. Although it seems to be able to defeat them, the Invisible Woman manages to find a nerve to shut down the android, and so they proceed to the Thinker himself.
The Thinker has an anti-matter shell locked on to each member of the Fantastic Four, and is telling them that he'll defeat them using it. However, just as he's about to shoot them, they suddenly deactivate, and Mr. Fantastic reveals that he told Willie Lumpkin to activate a certain bell downstairs, which deactivates all of the Fantastic Four's weaponry, a precaution made for if his lab was taken over. The Thinker is then arrested and the Fantastic Four resume their normal life.