Susan and Ben are helping Reed install new security equipment in the Baxter Building. Johnny is busy having H.E.R.B.I.E. add racing stripes and flames to the Fantasticar. They're interrupted when Iron Man, clad in one of his older gray suits, opens fire on the building. Ben is knocked off the building and Susan goes to her rescue. When Iron Man scratches the Fantasticar, Johnny attacks him. Reed confirms that the suit is worn by Tony Stark's bodyguard while Ben leaps onto their attacker. He fires a blast into Ben's face, knocking him loose. He falls onto the Fantasticar and Iron Man blasts Susan back. Angry, she cuts off the armor's helmet with a force field and they discover that it's empty. It continues to attack them and Reed confirms that it's operated by remote control. More Iron Man suits arrive and attack the team.
Reed tells the others to cover him and slips into the building. One suit follows him inside as Reed gets to his laboratory and manages to engage an EMP device. All of the suits shut down temporarily and then reboot and fly away. The others go inside and Reed explains that he tuned the EMP to the suits' frequency but they still managed to reboot. He insists that they go to meet with Tony Stark. En route, H.E.R.B.I.E. worries that Reed will reprogram him and asks Johnny for advice. Johnny suggests that he decorate Reed's lab with flames.
Tony Stark is in the middle of a meeting when the Fantastic Four arrive and enter through the window. Stark welcomes them in and Reed demands an explanation. Stark insists that the Iron Man armor couldn't attack them, and it's under the tightest security on the planet. They demand proof and he takes them to the security vault past their security systems. After several minutes, he gets the doors open and they discover that the suit is gone. An alarm goes off as a Doombot enters the vault and attacks them. It explodes but Susan protects them with a force field. The building starts to collapse and Stark runs off. A few seconds later, the real Iron Man arrives and lends a hand. Johnny attacks and Iron Man suggests they save the day first.
Once they've stabilized the building, Iron Man tells them that he'll take care of Dr. Doom and it's his problem now. When they suggest that he might need help, he arrogantly flies away. Reed insists that he'll need help. As they fly in pursuit, H.E.R.B.I.E. informs Reed that it's "quitting" on Johnny's secret advice. Reed realizes where Iron Man has gone and the team flies to the Latverian Embassy. Stark's bodyguard is fighting his armored counterparts and quickly shuts them down. However, as the team arrives, Dr. Doom emerges and reveals that he's wearing a modified suit of Iron Man's armor. He tells them to leave but Iron Man attacks. Doom takes remote control of his armor and commands him to attack on the Fantastic Four.
As they battle the controlled armor, Reed gets close enough to tell Iron Man that he needs to access his mainframe. Iron Man insists that they leave so he can handle Doom, but the Fantastic Four refuses. Reed wraps himself around the armor and explains that he knows Tony Stark is Iron Man, and that teamwork has its advantages. Stark reluctantly agrees but warns that Reed will need a supercomputer to run the computations. Reed contacts H.E.R.B.I.E., who refuses to help. Meanwhile, the others hold off Doom while Reed tries to convince H.E.R.B.I.E. he's just going to upgrade the computer. H.E.R.B.I.E. thinks about it as Iron Man breaks free of Reed's embrace. Sue rescues Reed and Johnny tells H.E.R.B.I.E. to access the mainframe. The computer does it, overloading itself in the process, and Iron Man is freed. Reed says they need a plan.
Doom defeats Johnny and Ben as Reed and the others arrive. Unimpressed, Dr. Doom tells Reed that the end is there. Iron Man blocks his blast with one of his own and the two grapple. Before Doom can stop him, Iron Man touches him and is knocked back. Reed explains that the armor is going to self-destruct. It explodes, leaving Dr. Doom badly damaged. He limps away, warning Iron Man that he has made a deadly enemy.
Later at the Baxter Building, Tony apologizes to the team and says that he hopes to return the favor one day. Later, Reed manages to repair H.E.R.B.I.E., who is eager to hear that his lab renovations met with his approval. Reed says that it does and notes that he's returned the favor. Johnny goes the garage and discovers that his car now is painted pink with flowers and teddy bears, and screams in anguish.