After believing Reed caused the cosmic storm accident on purpose Ben, Sue and Johnny are captured by Doom's robots while Doom steals Reed Richard's dimensional gauntlet to create a portal to the negative zone.
While showing off Reed's lab, Johnny and his latest girlfriend become trapped into the Negative Zone, infesting the Baxter Building with alien bugs in the process.
Philip Masters, a sculptor frustrated with his lack of recognition, gains the power to control people when a piece of the cosmic ray-bombarded space station falls from the sky and gives his clay the power to control people.
An energy sphere transports the Fantastic Four to the Negative Zone, where they are used by Doom to distract the insect conqueror Annihilus so that he can steal Annihilus's cosmic control rod.
Reed succeeds in reversing the Thing's condition, though the now-human Ben Grimm no longer has any memory of the team's transformation into the Fantastic Four.
After several attacks from Iron Man suits, the Fantastic Four track down Tony Stark. It turns out Doom was behind the attacks, and now the Four have to face both Iron Doom and Iron Man under Doom's control.
Frustrated by his repeated defeats at their hands, Ronan the Accuser asks the powerful Grandmaster to stage a contest that would give him the chance to beat the Fantastic Four.