Unknown De-mole-ition S1, Ep13 Unknown De-mole-ition An enormous subterranean creature attacks the Baxter Building looking for one of its eggs, which was secretly placed there by the Mole Man.
Molehattan S1, Ep15 Unknown Molehattan The Mole Man seeks out Ben Grimm as an ally as he pulls famous Manhattan landmarks down into his kingdom of Subterranea.
Strings S1, Ep16 Unknown Strings The Puppet Master uses his controlling clay to turn the city against the Fantastic Four.
Frightful S1, Ep19 Unknown Frightful A new super-powered quartet upstages the Fantastic Four.
Out of Time S1, Ep20 Unknown Out of Time The Fantastic Four return from a trip to the past to find Doom has changed history and is in control of the world.
Atlantis Attacks S1, Ep21 Unknown Atlantis Attacks Dethroned by Attuma the Barbarian, Namor turns to the Fantastic Four for help in reclaiming his kingdom.
Doom's Word is Law S1, Ep25 Unknown Doom's Word is Law While attacking the Fantastic Four, Doom's latest robot develops sentience.
Scavenger Hunt S1, Ep26 Unknown Scavenger Hunt Terminus, an enormous armored alien, arrives on Earth to plunder it of its resources.
Behold a Distant Star Unknown Unknown Behold a Distant Star
2006 Trial by Fire S1, Ep1 Sep. 2, 2006 Trial by Fire Johnny Storm is put on trial by Ronan the accuser against the Kree Empire.
Doomed S1, Ep2 Sep. 9, 2006 Doomed Doctor Doom switches his mind with Reed Richards, putting him in the perfect position to destroy the team.
Doomsday S1, Ep3 Sep. 16, 2006 Doomsday After believing Reed caused the cosmic storm accident on purpose Ben, Sue and Johnny are captured by Doom's robots while Doom steals Reed Richard's dimensional gauntlet to create a portal to the negative zone.
Hard Knocks S1, Ep4 Sep. 23, 2006 Hard Knocks Reed's effort to help his friend Bruce Banner brings the Four into conflict with the Hulk – and the people who are trying to capture him.
My Neighbor Was a Skrull S1, Ep5 Sep. 30, 2006 My Neighbor Was a Skrull
World's Tiniest Heroes S1, Ep6 Oct. 21, 2006 World's Tiniest Heroes Accidental contact with energy from a probe sent to the Microverse causes the quartet to start shrinking.
Zoned Out S1, Ep7 Oct. 28, 2006 Zoned Out While showing off Reed's lab, Johnny and his latest girlfriend become trapped into the Negative Zone, infesting the Baxter Building with alien bugs in the process.
2007 Imperius Rex S1, Ep8 Mar. 2, 2007 Imperius Rex Namor, the ruler of Atlantis, clashes with the Fantastic Four when he declares the world's oceans to be forbidden to humans.
Puppet Master S1, Ep9 Feb. 23, 2007 Puppet Master Philip Masters, a sculptor frustrated with his lack of recognition, gains the power to control people when a piece of the cosmic ray-bombarded space station falls from the sky and gives his clay the power to control people.
Impossible S1, Ep10 Mar. 9, 2007 Impossible One of Reed's returning space probes is followed by an annoying alien with the ability to turn himself into anything.
Bait and Switch S1, Ep11 Mar. 16, 2007 Bait and Switch An energy disruption during Reed's latest attempt to cure Ben causes the quartet to switch powers with each other.
Annihilation S1, Ep12 Jul. 14, 2007 Annihilation An energy sphere transports the Fantastic Four to the Negative Zone, where they are used by Doom to distract the insect conqueror Annihilus so that he can steal Annihilus's cosmic control rod.
Revenge of the Skrulls S1, Ep14 Mar. 23, 2007 Revenge of the Skrulls Ronan the Accuser gives a Skrull the powers of the Fantastic Four, who then uses them to defeat the super-powered team.
Doomsday Plus One S1, Ep17 Apr. 27, 2007 Doomsday Plus One Doctor Doom launches the Baxter Building into space.
The Cure S1, Ep18 Jun. 9, 2007 The Cure Reed succeeds in reversing the Thing's condition, though the now-human Ben Grimm no longer has any memory of the team's transformation into the Fantastic Four.
Shell Games S1, Ep22 Jun. 23, 2007 Shell Games 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.
Johnny Storm and the Potion of Fire S1, Ep23 Oct. 13, 2007 Johnny Storm and the Potion of Fire After exposure to a potion during a battle with the alchemist Diablo, Johnny finds his powers greatly increased – and his personality turning evil.
Contest of Champions S1, Ep24 Oct. 20, 2007 Contest of Champions Frustrated by his repeated defeats at their hands, Ronan the Accuser asks the powerful Grandmaster to stage a contest that would give him the chance to beat the Fantastic Four.