Johnny is put on trial by the Kree and Ronan the Accuser acts as judge. Reed, Sue and Ben help him, but Johnny gets a stay of execution by saving a Kree child in the trial's audience after a fight breaks out. The Supreme Intelligence notes the FF may be useful against the Skrull. 

Doctor Doom switches bodies with Reed, and Reed must stop him before he destroys the FF and turns the Baxter Building into a weapon. Of course, Sue, Ben and Johnny realize the truth, switch Reed and Doom's bodies back and thwart Doom's plan. 

Reed is accused of intentionally exposing the FF to the cosmic rays that gave them their powers. It turns out to be plot by Dr. Doom, and Ben forgives Reed after they save the world from Doom's plan of opening a dimensional portal where monsters will go around New York and destroy all human life. 

Bruce Banner visits Reed at the Baxter Building. Banner changes into the Hulk and the FF must stop his rampage in NYC and keep him from being captured by Agent Pratt who wants to use the Hulk for his own agenda. In the end, Pratt fails to stop Hulk and Hulk is loose in the badlands. Otherwise, the Fantastic Four have saved the day again. 

Skrulls impersonate the FF's neighbors in order to collect tissue samples from the FF. In the end, Skrull commander Kl'rt tells Ronan the Accuser all samples have been collected for him to begin making the greatest warrior the universe has ever known. 

One of Reed's microverse experiments causes the Fantastic Four to shrink putting them at risk when H.E.R.B.I.E. mistakes them for vermin and tries to exterminate them. The Fantastic Four are assisted by Ant-Man when it comes to getting to the lab and their lives are saved when they get to the lab with Ant-Man's help. 

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 as it multiplies and slowly destroys the Baxter Building, while Frankie and Johnny are trapped in the other dimension and look like they will be killed by worse versions of the bugs. In the end, Johnny and Frankie get back to Earth and the bugs are all put back to where they belong - except for one who remains in an old lady's fridge. 

Namor the Sub-Mariner arrives with a decree banning humankind from the oceans. Susan and Johnny go underwater to negotiate, but are taken prisoner in Atlantis. Ben and Reed must fight their way through sea monsters, Atlantean soldiers, and Namor to save their teammates. 

Alicia's stepfather acquires a supply of clay irradiated from a fallen piece of Reed's ill-fated space station that allows him to control others as the Puppet Master. 

The Impossible Man is brought to Earth by one of Reed's space probes and immediately starts causing trouble for everyone. In the end, the Fantastic Four convince Impossible Man that Earth isn't as fun as he is. 

Doctor Doom hijacks one of Reed's experiments and causes the FF to swap powers with one another. 

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. 

The Mole Man attacks the Baxter Building in hopes of luring the FF to his underground lair. 

The Skrulls now have the technology to duplicate the abilities of the Fantastic Four (due to secret help from Ronan the Accuser). They change their Commander Kl'rt into the Super-Skrull. As part of their deal, Commander Kl'rt gives Johnny to Ronan the Accuser to take prisoner. Soon, he manages to escape. However, now the Fantastic Four have to battle Ronan the Accuser and the Super-Skrull. 

The Mole Man is back. After kidnapping Ben, Mole Man attempts to get the Thing to join forces with him to create an underground paradise where appearances don't matter. 

The Puppet Master gets the city to turn on the Fantastic Four. The Four must clear their good names and stop the Puppet Master from taking over the minds of everyone on 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. 

Reed finally cures the Thing, but the cure also takes away all of his memories since the formation of the Fantastic Four. When the Mole Man attacks, She-Hulk must fill in for the Thing while the powerless Ben Grimm must find a way to save the day. 

The Wizard, Klaw, Trapster, and Dragon Man are the new team in town saving New York always one step ahead of the Fantastic Four. Reed begins to suspects that these Frightful Four are not the heroes they appear to be. 

The Fantastic Four return to New York to find that Doom has taken over the city and due to a change in history, they never got their powers. The Four must go back in time to set things right and to stop Doom. 

The Sub-Mariner returns, but this time he needs help to defeat Attuma, who has taken over Atlantis. While Reed, Susan, and Ben head off to help free Atlantis, Johnny stays behind and faces an attack on the city from a giant mutant whale. 

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. 

During a confrontation with Diablo, Johnny is exposed to a potion that makes him more powerful. Unfortunately, the potion also begins to turn him evil. 

The Grandmaster forces the Fantastic Four to battle Ronan the Accuser, Impossible Man, Annihilus, and Super Skrull. The fate of humanity depends on the winners of this mighty contest. 

Doctor Doom creates a super Doombot to face the Fantastic Four. The Four try and retrain this robot to be one of the good guys. In the end, Ben becomes the super Doombots friend, but then Doom's control is too strong and the super Doombot captures Susan and Reed. Johnny and Ben must save Susan and Reed, and fight Doom. But when Johnny is captured, Ben is left to fight the super Doombot. 

Terminus, an alien scavenger, comes to steal all of Earth's resources. While the Fantastic Four try to stop him, they realize he may be unbeatable.