Dr. Doom manages to transfer his mind into Reed's body by hacking his consciousness. Reed, who is now trapped in Dr. Doom's body, must now figure out a way to return to his friends and family, or else Dr. Doom will destroy the Fantastic Four and several city blocks by transforming the Baxter Building into his new weapon.

Reed stands accused of purposefully exposing Susan, Johnny and Ben to the cosmic rays that have transformed them into the Fantastic Four. While they're distracted by this turmoil, Dr. Doom strikes!

The Fantastic Four are brought to the Negative Zone where they come face to face with Annihilus. As if that wasn't bad enough, Dr. Doom arrives stealing Annihilus' power source and threatening Earth.

Doombots invade the Baxter Building in the middle of the night, but their attack is just a distraction for Doom to launch the Baxter Building into space.

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.