The Thing wakes up to find the Torch cooking breakfast for him… on his chest. Sue is more concerned about recent inexplicable news stories they're a menace. Reed wanders in saying he invented something he wasn't really aware of. The mayor and the police chief arrive to evict them, but the team is unaware that the Puppet Master is literally pulling their strings.
Out on the streets, Sue wonders that something is going on. Johnny screams as they take his car and Reed realizes that their security status across the city has been revoked. Sue finally fades them out and they take refuge in Alicia's apartment. They quickly realize that Alicia's father Phillip is responsible, but Reed needs his lab equipment to verify his involvement. They have Alicia check on her father, still in prison, while the team alternates their time between visiting old enemies and working new jobs. They return and find that Alicia hasn't determined anything, then kicks them out. The Puppet Master is controlling her as well, all from prison.
Phillip continues to manipulate the city against the Fantastic Four while controlling the guards in his prison with his radioactive clay. The team takes refuge in the riverside warehouse owned by Reed's father but the police surround them, having followed Johnny there. The police used enhanced weapons, armor, and robots provided by Reed, and Reed orders his teammates to stand down. He then makes a quick escape so he can clear their names.
The three remaining members are locked in a cell in prison while Phillip plays them a tape bragging of his plan. He tells them that he's been taking control of Reed all these weeks. The Thing bursts out but the mind controlled guards try to stop them and the team has to stop them without hurting them.
Reed covers conscious at the Baxter Building… with the Puppet Master accompanying him. Reed has unwittingly created a mind-amplification device for him and he puts it on, commanding the entire team to attack Sue, Johnny, and Ben. They manage to get past them to the Baxter Building, but the Puppet Master turns Reed against them. However, the others prove resistance to Phillip's mind control power and Reed manages to break free of his control. Reed reveals that the power amplifier enhanced cosmic powers, so Puppet Master's powers cancelled out against the team's powers.
After the Puppet Master is locked up in the high-security Vault, the city acknowledges the team as heroes once more. Phillip prepares to use some hidden clay, but Sue is there invisibly and relieves him of it.