| # | Title | Original AirDate(s) |
| 1 | "The Origin of the Fantastic Four (1)[1]" | 9/24/1994 | 101 |
| In an effort to raise money for education, The Fantastic Four tell Dick Clark the origin of their amazing powers, and their first confrontation with The Puppet Master, a villain who uses small clay replicas of people to take over their minds. In a running gag, the Thing tries various attempts to convince the audience to send in money for the charity. (Part 1 of 2) |
| 2 | "The Origin of the Fantastic Four (2)[2]" | 10/1/1994 | 102 |
| In an effort to raise money for education, The Fantastic Four tell Dick Clark the origin of their amazing powers, and their first confrontation with The Puppet Master, a villain who uses small clay replicas of people to take over their minds. (Part 2 of 2) |
| 3 | "Now Comes the Sub-Mariner[3]" | 10/8/1994 | 103 |
| Namor, Prince Of Atlantis grows tired of surface dwellers polluting his oceans. He rises from the ocean and kidnaps Sue Storm in order from her to become his queen. |
| 4 | "Incursion of the Skrulls[4]" | 10/15/1994 | 104 |
| An evil alien race known as The Skrulls invade the earth and impersonate The Fantastic Four in order to discredit them so they can take over the earth. |
| 5 | "The Silver Surfer & the Coming of Galactus (Part 1 of 2)[5]" | 10/22/1994 | 105 |
| A strange being known only as The Watcher warns The Fantastic Four of an oncoming threat, a giant named Galactus, who wishes to feed upon their world, and his herald, The Silver Surfer. Can The Fantastic Four save earth from the devourer of worlds? (Part 1 of 2) |
| 6 | "The Silver Surfer & the Coming of Galactus (Part 2 of 2)[6]" | 10/29/1994 | 106 |
| A strange being known only as The Watcher warns The Fantastic Four of an oncoming threat, a giant named Galactus, who wishes to feed upon their world, and his herald, The Silver Surfer. Can The Fantastic Four save earth from the devourer of worlds? (Part 2 of 2) |
| 7 | "Superskrull[7]" | 11/5/1994 | 107 |
| The Skrulls, angered at how easily Reed made their race look like fools, send an all-powerful Skrull to destroy them. How can The Fantastic Four beat an opponent who possesses all of their combined powers? |
| 8 | "The Mask of Doom (1)[8]" | 11/12/1994 | 108 |
| Dr. Doom kidnaps Sue Storm and blackmails the remaining Fantastic Four into doing his bidding in order for her to remain unharmed. Whilst Sue is held prisoner, she convinces Doom to explain his origins to her. (Part 1 of 3) |
| 9 | "The Mask of Doom (2)[9]" | 11/19/1994 | 109 |
| Dr. Doom kidnaps Sue Storm and blackmails the remaining Fantastic Four into doing his bidding in order for her to remain unharmed. Whilst Sue is held prisoner, she convinces Doom to explain his origins to her. (Part 2 of 3) |
| 10 | "The Mask of Doom (3)[10]" | 11/26/1994 | 110 |
| Dr. Doom kidnaps Sue Storm and blackmails the remaining Fantastic Four into doing his bidding in order for her to remain unharmed. Whilst Sue is held prisoner, she convinces Doom to explain his origins to her. (Part 3 of 3) |
| 11 | "Mole Man[11]" | 12/3/1994 | 111 |
| The Mole Man, a villain from the bottom of the world, sinks the Rockerfeller centre below group to kill The Fantastic Four, fearing only they are capable of stopping him from taking over the world. |
| 12 | "Behold the Negative Zone[12]" | 12/10/1994 | 111 |
| Reed accidentally opens a portal in the Baxter Building, as two opposing leaders from other worlds jump through the negative zone and declare war against each other over earth. |
| 13 | "The Silver Surfer & the Return of Galactus[13]" | 12/17/1994 | 113 |
| Dr. Doom returns and steals The Silver Surfers power cosmic. Now, with an unlimited amount of power, how can the Fantastic Four stop Dr. Doom. |
| # | Title | Original AirDate(s) |
| 14 | "And a Blind Man Shall Lead Them[14]" | 9/23/1995 | 201 |
| 15 | "Inhumans Saga (1): And the Wind Cries Medusa[15]" | 9/30/1995 | 202 |
| 16 | "Inhumans Saga (2): The Inhumans Among Us[16]" | 10/7/1995 | 203 |
| 17 | "Inhumans Saga (3): Beware the Hidden Land[17]" | 10/14/1995 | 204 |
| 18 | "Worlds Within Worlds[18]" | 10/21/1995 | 205 |
| 19 | "To Battle the Living Planet[19]" | 11/4/1995 | 206 |
| 20 | "Prey of the Black Panther[20]" | 11/11/1995 | 207 |
| 21 | "When Calls Galactus[21]" | 11/18/1995 | 208 |
| 22 | "Nightmare in Green[22]" | 11/25/1995 | 209 |
| 23 | "Behold, a Distant Star[23]" | 2/3/1996 | 210 |
| 24 | "Hopelessly Impossible[24]" | 2/10/1996 | 211 |
| 25 | "The Sentry Sinister[25]" | 2/17/1996 | 212 |
| 26 | "Doomsday[26]" | 2/24/1996 | 213 |
| # | Title | Writer(s) | Original AirDate(s) |
| 61 | "Secret Wars, Chapter I: "Arrival"" | John Semper &
Karen Milovich | November 7, 1997 (1997-11-07) |
| Madame Web sends Spider-Man to a planet, where the Beyonder tells Spider-Man he must pass a test to see who is stronger, good or evil. Beyonder sends evil, aka Red Skull, Alistair Smythe, Doctor Doom, the Lizard, and Doctor Octopus, to a planet, and causes a year to pass. Chaos is a result. Spider-Man's job is to save the planet. He's sent to the world, and Beyonder tells him he gets to have help. Spider-man can bring heroes, from anywhere. Spider-Man calls for the Fantastic Four, Iron Man, Captain America, and Storm. Later, the Lizard attacks them. The team eventually stops him. Later, Mr. Fantastic helps the Lizards turn back into Curt Conners. Lizard then joins the team, and the episode ends. Part 1 of 3. |
| 62 | "Secret Wars, Chapter II: "The Gauntlet of the Red Skull"" | Virginia Roth | November 14, 1997 (1997-11-14) |
| Spider-Man summons the Black Cat from Earth. The heroes launch an attack along with the local colonists, against the Red Skull who is assisted by Alistair Smythe and Doctor Octopus. The strike force for the team is Spider-Man, Black Cat, Captain America, Lizard, and Iron Man. When they go to Skull's fortress, Skull sends his newly built Cyber Skulls, and Spider Slayers. Allister Smythe wanted to go back to Earth because he wants to find his father. So, he joins the heroes and self-destructs the robots, and the heroes get inside the fortress. Seeing their fortress destroyed Red Skull and Doctor Octopus escape. Part 2 of 3. |
| 63 | "Secret Wars, Chapter III: "Doomed"" | Ernie Altbacker,
John Semper &
Mark Hoffmeier | November 21, 1997 (1997-11-21) |
| This episode opens up with Spider-Man and the Lizard going to help the Fantastic Four in their battle against Doctor Doom. When they arrive at the location, Doom's robots had kidnapped the Thing. Later the heroes defeat Doctor Doom and the Beyonder returns saying the game is over. He transports them all out into space and says that they did excellent in the Secret Wars, and that the heroes (not counting Spider-Man) will not have any recollection of what happened. Beyonder tells Spider-Man that since this warm-up task has finished, then now it is time for the real task. Part 3 of 3. |
