A meteor from deep space landed on a remote farm, and after Reed studied it back at the Baxter Building, he discovered that it had energy-absorbing properties. As the meteor was sealed in the lab's vault, the team noticed a strange green glow outside, and an individual calling himself the Molecule Man performing seemingly impossible feats. He proclaimed himself leader of the city, but the Fantastic Four quickly appeared to challenge him. He told the team that he was once a lab technician who was transformed in an atomic accident, and now had the power to rearrange all molecules. The Molecule Man then met with the Pentagon and forced them to accept his rule. Reed developed an electrode gun to prevent Molecule Man's powers from working on specific objects, while the villain himself took over the city. Reed managed to drive the Molecule Man off with the use of the electrode gun, and then used it to coat one of the last tanks unaltered by him. The team then used the tank to confront the Molecule Man for the final battle.
An alien ship from deep space approached Earth and abducted the Fantastic Four. The robotic crew took the super-team to their world, where Reed was informed that he and the rest of the Four were being charged with crimes against evil, with the team's accusers being Klaw, Molecule Man, and Blastaar. The Court of Evil observed Reed's own memories of the team's battled against Klaw, Molecule Man, and Blastaar, while the rest of the team escaped their confinement. Reed was judged guilty and sentenced to disintegration, but Ben, Johnny, and Sue rescued him. The Four then have to face the three super-villains in addition to the planet's evil judge and robot army.