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!

Upon returning from a mission, the team finds their neighbors in the Baxter Building much more friendly than usual, but it soon becomes clear their "neighbors" are shape-shifting aliens - the Skrulls!

Reed's miniaturization experiment malfunctions, shrinking the team and putting them at risk when H.E.R.B.I.E. incorrectly identifies them as vermin and tries to exterminate them.

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.

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 and Namor to save their teammates.

When Reed recall one of his deep-space probes, it brings back with it the Impossible Man. The Fantastic Four must find a way to get rid of the annoying imp before his antics become dangerous.

Dr. Doom causes an energy surge during one of Reed's experiments. As a result the Four have swapped powers with one another. Now the team must face Doom with new and untrained skills.

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 sends a giant monster to attack the Baxter Building, hoping to lure the Fantastic Four into his kingdom of Subterranea.

The Four have a contest called "Fantastic Fifth for a Day." But when the Skrulls return with the Super Skrull, it may be up to nerdy teen Rupert, the Fantastic Fifth, to save the day.

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.

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 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.

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.

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.