Mumm-Ra creates device that can make Panthro clones. He embeds the spirit of Hammerhand into his clone and sets it free to destroy Third Earth. The Third Earth inhabitants blame the Thundercats for the terror because they think its the real Panthro destroying their villages and burning their crops. The real Panthro finally encounters his clone and, with the help of Lion-O, manages to destroy it. Enraged about his defeat, Hammerhand destroys Mumm-Ra's cloning device.

Wilykit and Kat accidentally free an ancient monster that was banished to an old shrine centuries ago. The evil monster, Mongor, begins to destroy the planet, and is much stronger than the Thundercats. He captures all the elder Thundercats with his powers. Wilykit and Kat return to the shrine to find a way to destroy him. They report back to Lion-O and tell him that in order to destroy Mongor, he has to fight the monster without looking at it. Lion-O defeats the monster and all is returned to normal.

The Thundercats briefly show Lion-O how the time capsule they recovered from the caveman works. Curious to see more, Lion-O activates it during his night-time watch, and gets caught in its projection rays. The rays send him back in time to Thundera, just before the final tremor that destroyed the planet. Meanwhile, the Mutants have built an evil robot monster that is destroying Cats' Lair. Back on Thundera, Lion-O encounters his father, Claudus, and saves him from a Mutant attack. In return, Claudus gives Lion-O the plans to the robot that was attacking the Thundercats in his own time.

An old scientist seeks the Thundercats to help him save the oceans of Third Earth. Long ago, a crack was made in the bottom of the ocean which caused the water to drain into the earth's core. Dr. Dometone created a plug which sealed the hole in the ocean, and saved Third Earth from destruction. Now, an evil miner, Scrape, has come to remove the plug and mine the rock that is found on the bottom of the ocean. The Thundercats join Dr. Dometone and his frog-like robot, Herkie, to save the planet from total destruction.

Jaga is captured by Nemex, an evil being in the Astral World, and Lion-O tries to find a way to rescue him. Third Earth legend says that the only person who can transport anyone to the Astral world is the evil Nether-Witch. Little do the Thundercats know that Mumm-Ra and the Nether-Witch are one and the same. Mumm-Ra traps Lion-O in the Astral world, and Lion-O sets out to save Jaga. While escaping the Astral prison, Lion-O and Jaga save an old sorcerer named Brodo who has been imprisoned in the Astral Prison for centuries. As thanks, Brodo sends Lion-O back to his own dimension.

The Thundercats think that Snarf is getting too old, and that he is not up to doing as much as he does. To prove them wrong, Snarf saves the Thundercats from another mess. The evil Crystal Queen, Tartara, captures the Arrietta bird, whose songs enchant the Berbils' harvests. Lion-O, upset with her selfishness, goes off to save the bird, but gets caught and put under an evil spell. Snarf, managing to slip through the crystal queens defenses, saves Lion-O and frees the Arrietta bird.

Nearly all the Thundercats have been captured by the Mutants and imprisoned in Mumm-Ra's Pyramid, forcing Snarf to use his own talents to free them.

An alien spaceship crash lands on third earth, and it can somehow communicate with Cheetara through her sixth sense. She becomes a part of the spacecraft, and begins to feel what it feels. The Mutants recover the space ship, and begin tampering with it. Little do they know that it is not only affecting the spaceship, but it is affecting Cheetara. In order to save Cheetara, the Thundercats set out to recover the space ship from the Mutants and fix it.

Mumm-Ra summons the great samurai Hachiman to seek and destroy Lion-O. He tells Hachiman that Lion-O and the Thundercats are destroying his planet. Hachiman and Lion-O confront each other, but their swords refuse to draw on each other. They become allies and hope to destroy Mumm-Ra together. Enraged, Mumm-Ra summons another warrior, a ninja, to sabotage the Thundercats, and retrieve Slithe, whom they have captured.

Vultureman summons Ratar-O to take him to the planet of the Snarfs to capture one of them and use it as ransom with the Thundercats. Snarf, thinking his entire race was wiped out when Thundera blew up, finds out that they have captured Snarfer, his little nephew. The Thundercats set out to find the Mutants and save Snarfer. After successfully saving Snarfer, the Thundercats are faced with the problem of returning Snarfer to his planet. Panthro cleverly invents the Feliner, a spaceship. In order for it to work, though, the machine need a hyperspace mega-condenser. Snarf reminds him that there is one on Ratar-O's Ratstar. The Thundercats once again pursue the Mutants to the wreckage site of the Ratstar to take their mega-condenser.

Vultureman summons Ratar-O to take him to the planet of the Snarfs to capture one of them and use it as ransom with the Thundercats. Snarf, thinking his entire race was wiped out when Thundera blew up, finds out that they have captured Snarfer, his little nephew. The Thundercats set out to find the Mutants and save Snarfer. After successfully saving Snarfer, the Thundercats are faced with the problem of returning Snarfer to his planet. Panthro cleverly invents the Feliner, a spaceship. In order for it to work, though, the machine need a hyperspace mega-condenser. Snarf reminds him that there is one on Ratar-O's Ratstar. The Thundercats once again pursue the Mutants to the wreckage site of the Ratstar to take their mega-condenser.

Mandora, on space-patrol, encounters an old pirate ship which doesn't meet inter-galactic standards. She boards the ship, arrests the pirate, and sends the ship to a space prison . Little does she know that she has boarded the Jolly Roger, the home of the evil Captain Cracker. Mandora is captured by the creature. Lion-O intercepts one of her distress calls, and must go into space to save her -- easier said than done, as Cracker orchestrates a prison break.

The Driller, Mumm-Ra's servant who captured Panthro for him in Spitting Image, returns to aid Mumm-Ra once again. His job this time is to drill a hole from the Cats' Lair to the Acid lake, allowing the acid to flow in and eat away at the lair. The Thundercats set out to find the one substance that neutralizes the acid.

Wiz-Ra, Mumm-Ra's enemy from long ago, comes back every 7000 years through a portal that just happens to be in Cheetara's bedroom. Wiz-Ra wears a magical helmet that lets him control minds. When the time arrives and Wiz-Ra comes through the portal, Mumm-Ra steals the helmet. Cheetara helps Wiz-Ra get the helmet back and free the ThunderCats from its spell.

Mumm-Ra finds out that the Kingdom of Webs has a new Queen, Spidera. Mumm-Ra thinks he can lure Lion-O into her lair. He transforms into a diamond fairy and casts a spell on Lion-O. Snarf follows them and gets trapped in the Kingdom of Webs. Lion-O tries to save him but ends up having to call the other Thundercats. Eventually they confront and beat Spidera.

Mumm-Ra hires Captain Shiner no send a fake distress signal to the Thundercats. With their new vehicle, the Feliner, the Thundercats set out into deep space to help the "ship in distress". When they arrive, Shiner captures Lion-O and the Sword of Omens. He gives the Sword to Mumm-Ra, and Mumm-Ra throws it into a black hole. Cheetara returns to Third Earth to get Panthro. They rescue Lion-O, and seize Shiner's ship. Panthro sets a course into the black hole to recover the Sword. They enter, and must battle the robotic city of lost space ships to recover the Sword of Omens and escape.

Wilykit and Kat find an ancient harp that has a genie in it. His name is Charr-Nin. Mumm-Ra appears to the genie and tells him that if he destroys the Thundercats, he will be freed from his eternal prison in the harp. Foolishly, Char-Nin agrees, and begins trapping the Thundercats in his harp one by one. Mumm-Ra's plan works, and he betrays Charr-Nin. During their arguing, the Thundercats manage to escape, leaving Mumm-Ra and Charr-Nin battling beneath the earth

On Lion-O's 20th birthday, he must pass a set of trials to become the true Lord of the ThunderCats. Even though he is the hereditary Lord of the ThunderCats, he must prove himself to be worthy of that title. His first test is to beat Panthro in a duel to test his strength.

A vagabond space traveler lands on Third Earth to challenge Mumm-Ra to a fight. The Demolisher is victorious against Mumm-Ra and sends him running back to his tomb. Mumm-Ra acknowledges the power of the Demolisher, and convinces him to seek and destroy Lion-O. The Demolisher, searching for another fight, gladly accepts Mumm-Ra's advice. He battles with Lion-O only to face defeat.

Monkian goes to Mumm-Ra and agrees to give him anything if Mumm-Ra will make him powerful enough to rule Third Earth. Mumm-Ra agrees, and gives him Power Spheres which make him super strong and give him super weapons. He freezes all the Thundercats, then defeats Lion-O and takes the Sword of Omens back to Mumm-Ra. Mumm-Ra takes it, and then says that Monkian's part of the bargain will be that he can keep the spheres, but he has to stay in Mumm-Ra's pyramid for all eternity. Walls surround Monkian, and every time he breaks them down, a new set of walls shows up. While Monkian and Mumm-Ra are arguing, Lion-O retrieves the Sword and frees the other Thundercats. Monkian gives up his power to be free again.

After the Mutants fail to ambush and defeat the Thundercats with Vultureman's new Thundrainium cannon, Vultureman, furious about the failed attempt and the loss of his weapon, activates a self-destruct built into each of his inventions or repaired machinery, and all the Mutant technology disintegrates. To even the odds, Slithe asks Mumm-Ra to send an electrical energy creature to destroy all the equipment in Cats' Lair, which also seals up the door to the Sword Chamber, trapping the Sword of Omens inside along with all the Thundercats' weapons. The Mutants attack, and manage to capture Cheetara and Panthro. Snarf must climb into the ventilation shafts to reach the Sword Chamber from within, but Jackalman follows him, trying to capture him. Outside, Lion-O is attacked by Slithe and Monkian, and later Mumm-Ra. After Snarf successfully gets the Sword back to Lion-O, Lion-O frees Panthro and Cheetara and they defeat Mumm-Ra and the Mutants.

Micrits, a tiny race of human-like figures, happen to live right outside Cats' Lair. Unaware of their existence, Lion-O manages to continuously step on their village and destroy their homes. Upset at this disrespect, the Micrits decide to take a stand and manage to trap Lion-O. With the Thundercat Lord in trouble, the Mutants attack Cats' Lair. After much talk, Lion-O manages to convince the Micrits that he is a "good guy" and convinces them to let him go to help save his friends. Once again, Lion-O saves the day, and befriends the Micrits.

On the second day of his trials, Lion-O must race Cheetara through the dangerous lands of Third Earth. Although Cheetara is by far the fastest among the Thundercats, her speed can only last for a short time period. Lion-O takes a shorter but more dangerous route to make up for Cheetara's advantage.

Mumm-Ra awakens the Rock Giant, an ancient monster made of stone which looked like a mountain to the TCats. When it wakes up, Mumm-Ra sends it to destroy Cats Lair. The TCats try and defeat it using the Thundertank, and eventually with the help of the Sword, the giant is beaten.

The normally submissive JackalMan decides to start his own army in hopes of conquering Third Earth by himself. He does manage to give the Thundercats trouble, but soon he is defeated and ends up crawling back to the other mutants at Castle Plundarr, who weren't very happy that he rebelled in the first place.