Lion-O becomes homesick, and his memories of Thundera are almost nonexistent. Jaga appears to Lion-O and tells him that on their spaceship, they brought with them a time capsule which contained a recording of Thundera and its history up to the time it was destroyed. The Thundercats set out to search for their time capsule.

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.

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.

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.

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.

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.

Panthro invents flying video cameras which are suppose to record the events that take place on third-earth so they could create their own holographic time capsule. Mumm-Ra, in hope of destroying the Thundercats once more, revives the great mechanical monsters which the Thundercats have destroyed in the past to attack them. He revives the Mutant War robot, The Driller, The Giant Insect, and the Techno-Pede.

The story of Excalibur, the greatest sword in history, is revealed to Mumm-Ra, who is then determined to find the Excalibur and defeat Lion-O and the Sword of Omens.

A Terator Starship, an extremely ugly spaceship, is pursued by a Kymera Craft, a visually appealing spaceship. The Terator Spaceship escapes and lands at the Cats' Lair

Mumm-Ra learns about the Treasure of Thundera and the Sword of Plundarr (Jaga had beaten Ratilla, who owned the Sword, and then buried the sword deep underground), and he and Ma-Mutt ""travel back in time and space"" to explore the debris of Thundera and look for the sword, which causes the planet to reform. The Thundercats find out about this and must make the journey to New Thundera to stop Mumm-Ra. Lynx-O and the Thunderkittens are left at the tower while the other Thundercats at the Lair are preparing the Feliner for the trip to New Thundera. Vultureman notices that the tower is only guarded by 3 Thundercats and goes to Sky Tomb and tells Luna. Luna then sends Red Eye and Tug Mug to attack the Tower, and they capture Lynx-O and the Thunderkittens.

Lion-O and the other Thundercats arrive and save Lynx-o and the Thunderkittens from Red Eye and Tug Mug. The Thundercats learn more about New Thundera, especially the dangerous places affected by the moons of Plundarr where the Lunataks come from. The Thundercats must develop special equipment and clothing to counter those dangers. Also, they learn that all the snarfs have been turned into slaves and Snarf and Snarfer want to rescue them no matter what the cost. Vultureman learns of the Thundercats plan, so he abandons the other Mutants and takes the Rat-Star. But Slithe has snuck aboard. Right after the Feliner takes off, the Rat-star ambushes them and it seems all over for the Thundercats aboard the Feliner. Lion-O uses the sword to free everyone and along with Ben-Gali and Wilykit on the HoverCat, go after the Ratstar and it crashes on Hook Mt. The Thundercats leave Third Earth's atmosphere and Lynx-O tells him that Mumm-Ra has already located the Sword of Plundarr.

Mumm-Ra retrieves the Sword of Plundarr and the Thundercats arrive on New Thundera. While the Thundercats want to get the Sword and treasure, Snarf and Snarfer want to free their fellow snarfs. While the Thundercats sleep, Snarf and Snarfer sneak away, but are discovered and captured by Mumm-Ra. He disguises himself as Snarfer and he leads the Thundercats to where the treasure is located, but it can only be freed by the Sword of Omens. Once the treasure is freed, Mumm-Ra reveals himself and defeats the Thundercats with the Sword of Plundarr. Now Mumm-Ra possesses the Sword of Plundarr and the Treasure of Thundera

Mumm-Ra tries to get away but the Sword of Omens breaks open the casket dropping the treasure all over the planet, and Snarf, Snarfer, and one other snarf escape. Mumm-Ra gives a false Book of Omens to Ma-Mutt, Slithe and Vultureman, who have arrived on New Thundera in the Rat-star, for safe keeping so that he can decipher the real Book of Omens. The Thundercats go after them through the Caverns of Cold. They head toward the Canyons of Youth, but due to the effects of the canyon, Panthro, Cheetara, Tygra, Snarf, and Snarfer are changed into Thundercubs. Lion-O must use the sword to give the Thundercubs Thundercat understanding. Meanwhile on Third Earth, Jackalman, Monkian, and the Lunataks attack Cats Lair and capture Ben-Gali and Wilykit. Lion-O learns that the Thundercats back on Third Earth are being held prisoner in Sky Tomb, so he decides to send the Thundercubs to Third Earth to rescue them while he tries to get the Book of Omens from Mumm-Ra. Snarf decides to stay with Lion-O an

Lion-O frees the Thundercubs from Mumm-Ra's spell and the Thundercubs safely leave New Thundera. Lion-O and Snarf must confront Mumm-Ra and get the Book of Omens. After they defeat Mumm-Ra, they ask Mu-Mutt (using a magical flute) to use Mumm-Ra's ""device"" to get them back to Third Earth. Meanwhile the Lunataks capture some Berbils and the Thundercubs return to Third Earth and they and the Thunderkittens must go to Sky Tomb to free the other Thundercats and the Berbils. After everyone is freed, they are all cornered by the Lunataks, but Lion-O and Snarf arrive to save the day. The Thundercubs must then go in the Cave of Time to become Thundercats again and Mumm-Ra is abandoned on New Thundera and the Ancient Spirits bring him back to Third Earth.

After looking at the Book of Omens, and seeing a picture of a necklace, Lion-O discovers that there are pictures of the Thundercats on the necklace. Jaga appears to Lion-O and tells him that he is looking at a picture of the Chain of Loyalty. Jaga tells Lion-O that if the chain gets broken, it would cause the Thundercats to turn against each other. In hearing this, Lion-O and the Thundercats (Panthro, Tygra, Cheetara, and the Thunderkittens) set off to Thundera to find the chain. Mumm-ra, eavesdropping on Lion-O through his pool at the pyramid, goes to Thundera, kidnaps and disguises himself as Snarf. When the Thundercats arrive, they split up into groups to find the chain, and Mumm-Ra goes with Lion-O and the Thunderkittens. Lion-O's group finds the chain and Mumm-Ra gets it, breaks it, and returns to his true form. For a while, the Thundercats, except Lion-O, fight against each other until Lion-O uses the sword of Omens, which magically puts the necklace back together. Mumm-ra is def

The Ancient Spirits of Evil give new life to Mumm-Ra and Ma-Mutt, send them to New Thundera, and build a new Pyramid for Mumm-Ra. The Thundercats say goodbye to Third Earth and depart for Thundera, leaving Tygra and Pumyra behind to watch Cat's Lair and the Tower of Omens. The Thundercats soon arrive and begin plans to build a new lair. Mumm-Ra meanwhile learns that the planet's gravity is controled by the Gyroscope under the Churning Rocks at the center of the planet. The Gyroscope is guarded by Jaguara, an ancient Thundercat sorceress. Mumm-Ra disguises himself as Jaga and puts Jaguara under a spell, making her change the rotation of the Gyroscope to throw the Thundercats clear off the planet. As the Thundercats are floating away, Lion-O calls on the Eye of Thundera to help him, and it breaks Mumm-Ra's spell... but not before Mumm-Ra takes part of the Gyroscope's regulator. Without those controls, the planet will be destroyed within 2 hours...

More and more earthquakes are ocurring because of the malfunctioning Gyroscope. Meanwhile Lion-O recieves a distress signal from Thunderian refugees, and he, Cheetara, and Snarf go to find them. Mumm-Ra resurrects Grune the Destroyer, and Grune seeks out Lion-O and Cheetara. Grune finds and fights them, breaks the Sword of Omens, and then he chains them up on the Churning Rocks. Snarf, who was hiding, gathers the pieces of the Sword to take back to Bengali to be fixed. Snarf gets captured by Char, a theif who wants the Sword for himself. Snarf tricks him into reforging the Sword, and when it is as good as new, Lion-O begins to sense it, and so he calls it. The Sword goes to him, he escapes, and then he defeats Grune. But Mumm-Ra still has the Gyroscope's regulator...

Lion-O, Panthro, and the Thunderkittens take the Whisker, a new flying vehicle, to the Churning Rocks to rescue the Thunderian refugees who had called from there. The Thundercats get captured by Two-Time, a robot with 2 heads. Two-Time takes them aboard his spaceship, Dome-Down, and the Thundercats see that he has also captured the refugees. Lion-O defeats Two-Time and the refugees are freed. Meanwhile, Lynx-O, Cheetara, and Bengali spot Mumm-Ra near the Churning Rocks, and inform Lion-O of this. Lion-O, Panthro, and the Thundekittens head to the Churning Rocks and confront Mumm-Ra, who is in the form of Jaga again. They break Mumm-Ra's spell (again) over Jaguara, who had temporarily repaired the Gyroscope. Lion-O defeats Mumm-Ra, but Mumm-Ra reminds them all that eventually the planet will be destroyed without the real controls, which he still has...

Mumm-Ra sends Ma-Mutt disguised as Mandora to free the Mutants from Capt. Bragg's circus train and sends Bragg and Crowman falling into deep space. The Mutants are then ordered by Mumm-Ra to get rid of Tygra and Pumyra. The Mutants attack Snowman on Hook Mt. and Snowmeyow gets Pumyra for help and Tygra contacts the real Mandora to save Bragg and Crowman. Then together, they recapture the Mutants. Meanwhile on New Thundera, the earthquake tremors grow worse and the new Cats Lair collapses trapping Snarf in the ruins. Lion-O uses the sword to contact the other Thundercats and they rush to the Lair to save Snarf. Afterwards, Mumm-Ra destroys the Gyroscope's regulator...

After another earthquake caused by Mumm-Ra ruins the new Cats Lair construction site, the Thundercats go to see Jaguara and confront Mumm-Ra. Unfortunately, Mumm-Ra puts up a force field over entrance. Jaga appears to Lion-O and tells him to use the Eye of Thundera to get to Jaguara and the Gyroscope. Lion-O does so and battles Mumm-Ra, who throws him into the bottomless pit underneath the Gyroscope. Lion-O however, manages to throw his grappling hook to the top, which pulls him back up. Lion-O then shines the signal, which goes through the force field. All the Thundercats leap through the signal which takes them through the force field. Together, they fire all their weapons at Mumm-Ra and he is defeated. But before he leaves, he breaks the cord that holds the Gyroscope above the pit and it falls through. Now, New Thundera is literally falling apart. But Lion-O throws the sword in the spot where the Gyroscope used to be and calls upon the Thundercat Ancestors for help. The sword starts

Wily Kit and Kat, exploring New Thundera, stumble upon an Orb of Gold, and pick it up thinking that it is apart of their Heritage. Possessed by the power of the Golden Sphere of City, the ThunderKittens get greedy, and let the power of the orb overcome them. Mumm-Ra manages to get a hold of the orb, and his powers get four times more powerful. He gets so powerful, he destroys the Sword of Omens. Jar, the scrap metal collector reforges it for Lion-O. He gets so powerful that he challenges the power of the ancient spirits of evil. They lock him out of his pyramid until he surrenders the Orb to them. The spirits of evil let him back in, but destroy the Golden Sphere of City.