Due to the line of Kree Sentries - alien robots that have been observing the Fantastic Four - having been destroyed, Johnny is put on trial by Ronan the Accuser against the Kree Empire. Ben and Susan are set to defend him, and Reed is chosen as his lawyer. However, since Johnny is already presumed guilty before the trial starts, it's not going to be easy.
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.
Things take a turn for the worse when Johnny gives his friend Frankie an unauthorized tour of Reed's lab. When Frankie is sucked into another dimension, Johnny goes in after her to prevent anyone from finding out. But as he does so, a small bug comes through the dimensional portal. Susan, Ben, and Reed now have to deal with the bug, while Frankie and Johnny are trapped in the other dimension.