Doom has been missing in action ever since he got stuck in Hell, so neighboring Hungary invades Latveria(?!?) and the Fantastic Four intervene to stop them and save the Latverians from having to live under Hungarian rule. (Is Hungary really that bad? Why wouldn’t a bunch of other countries want to run in and take all of Doom’s cool tech? Yes, the plot of this arc is a little baffling—for so, so many reasons.)
The foursome capitalize on the sample of Doom’s hair that Reed got in the last arc. I’m still a little confused about why Reed wouldn’t have already had some Doom DNA, given the sheer number of times they’ve faced off, switched bodies, etc. But anyway, he has it so that he can trick Doom’s robotic defenses into thinking Reed is the Doctor. Once inside his fortress, they start rummaging through his stuff—although it turns out Doom destroyed a lot of it before he was sent to Hell. The FF also decide to stay in Latveria and rule in Doom’s stead.
Reed makes himself king. An interesting parallel: Right around the time The Avengers start working for the U.N. and becoming the world’s police force, the FF move to Latveria to take it over and right the “wrongs” that they think were created by Dr. Doom’s reign. Also at the same time Iron Man, in his own series, is becoming the U.S. Secretary of Defense. Interesting. Also, paralleling contemporary, real-life missions like the U.S.’s attempt to “free” Iraq from Saddam Hussein and Pakistan from the Taliban, Reed finds that the native Latverians are not welcoming.
But he perseveres, destroying nuclear weapons hiding deep below the country and becoming increasingly authoritarian.
It turns out that Doom’s soul is still connected to his homeland. Doctor Doom frees himself from Hell by putting his soul in Susan’s body at the same time that Nick Fury leads a covert action to depose Richards as king. Fury and Reed try to fight Doom off, but he jumps into Johnny’s body and then into Thing, who he tries to force to kill Johnny.
And Reed does. Reed shoots Thing to stop him from killing Human Torch, forcing Doom to flee the body (and presumably return to Hell).
Now, unlike when Jonathan Hickman killed the Human Torch, Mark Waid knows damn well nobody is gonna believe that Thing is dead. It’s not really good commercial drama to kill a major character with movie potential. (The only time this really worked in Marvel history is when Ed Brubaker killed Cap, and that was because he let the dude stay dead for years.) So instead of making the book a big “let’s mourn Thing even though we know he’ll be back before the next movie” charade, Waid uses it as an excuse to explore the concept of death and God in Marvel comics. That’s the next story arc.