With the Mutants and Lunataks gone, the Ancient Spirits of Evil give Mumm-Ra until sunset to destroy all the Thundercats, and to prove they're not bluffing, they exile Ma-Mutt. Mumm-Ra spreads destruction all over Third Earth, sends Tygra, Cheetara, and Panthro to limbo, and buries Lion-O alive. Then he attacks and destroys the Tower of Omens, and the Thunderkittens barely escape, but Mumm-Ra sends them to limbo too. Snarf must go into the Book of Omens to find out how to defeat Mumm-Ra. Jaga and the Thundercats in limbo go into the Eye of Thundera to help Lion-O free himself from his rocky prison. Lion-O then battles Mumm-Ra at Cats Lair and finds out from Snarf that Mumm-Ra only has until sunset to defeat the Thundercats. Mumm-Ra fails and the Ancient Spirits of Evil banish and exile Mumm-Ra from Third Earth. With all their enemies gone, the Thundercats decide to permanently return to New Thundera

The Mutants, who have also reached Third Earth, encounter an old pyramid. It turns out to be the home of Mumm-Ra the Ever-Living, and they join forces to capture the Sword of Omens. Both the Mutants and Mumm-Ra attempt to attack Lion-O to possess the Sword, but miserably fail.

With their home planet, Thundera, about to explode, the Thunderians flee to a distant galaxy. Before they can make the long journey the Mutants sweep in and destroy most of the fleet in an attempt to capture the Eye of Thundera. Due to the attack, the Thundercats find themselves on a distant planet. A grown-up Lion-O must save his Thundercats from the Mutants on Third Earth.

Mumm-Ra uses his shapeshifting abilities to pass himself off as a Thunderian so he can stage the "rescue" of Cheetara and infiltrate Cats' Lair.

With only Lion-O and Snarf guarding the Lair, Mumm-Ra decides this is a perfect opportunity to invade the Lair, so Ma-Mutt captures Snarf and Mumm-Ra switches Snarf and Ma-Mutt. Ma-Mutt (who now looks like Snarf) goes to Cats Lair and gives Lion-O some poisoned candy fruit. Lion-O becomes ill and realizes that this Snarf is really Ma-Mutt and Mumm-Ra arrives and defeats Lion-O. Snarfer's bad dream of Snarf becoming a dog causes him, Ben-Gali, and Pumyra to go to Cats Lair, but Mumm-Ra lays a trap for them. He sends Ma-Mutt to get Snarfer and Lion-O becomes better again and distracts Mumm-Ra. When Lion-O summons the other Thundercats, Snarf (who looks like Ma-Mutt now), using Mumm-Ra's chant that changes Mumm-Ra into the everliving, becomes... Snarf-Ra the everliving and he rescues Ben-Gali, Pumyra and they in turn rescue Snarfer from Ma-Mutt. Then Snarf-Ra challenges Mumm-Ra and defeats him. After the battle is over, Lion-O uses the sword to restore Snarf to his original state.

Vultureman creates a weapon that shoots pure Thundrainium in hopes of destroying the Thundercats. His first victims are the Thunderkittens who fall into a deep cavern and become injured. Lion-O and Snarf search for the missing kittens. Meanwhile Vultureman must get more Thundrainium from Chilla in Darkside and is also ordered by Slithe to fix the Mutants' machines. The Thunderkittens are saved by a Wollo and they discover that the Wollo village has been ""iced"" and they are captured and used as bait to lure Lion-O. When Lion-O and Snarf arrive, they are shot down by Vultureman's weapon and Lion-O becomes weak and summons the Thundercats. Just as Vultureman is about to finish off Lion-O, Ben-Gali arrives, wrecks Vultureman's weapon and drives the Mutants and Chilla away. Lion-O then uses the sword to restore the Wollo village.

With their supply of Thundrillium running low, the Thundercats set off in search of a fresh supply. Tygra detects a large deposit in a cave and goes to investigate - unfortunately, he has entered the Cave of Time and anyone who ventures in there will age rapidly until they die. His only hope is that Cheetara's speed will be fast enough to allow her to escape the Cave's effects.

Wilykit and Wilykat try to stop a band of living gargoyles from robbing a Wollo but fail to do so and trail the gargoyles to a nearby Tower. Wilykat is trying force the door open when he suddenly disappears, leaving Wilykit - who was looking for another way in - close to panic. She and Lion-O (alerted by the Sword of Omens) must now brave the Tower's potentially lethal traps in order to rescue Wilykat.

Mumm-Ra plays deception with the Thundercats when he (disguised as Jaga) tells Lion-O that the Thundercats at the Tower of Omens will rebel and take Third Earth for themselves. Then he disguises himself as a Tuska warrior and asks the Thundercats at the tower for help. Ben-Gali, Pumyra, and Snarfer go to investigate while Lynx-O calls on the others to help, but Lion-O warns the others of their possible treachery, but Panthro, Cheetara, and Snarf go anyway but somewhat cautious. When they meet, the Tuska warrior "accidentally" causes the newer Thundercats to attack. He then disappears and the Thundercats start fighting each other. Meanwhile the Lunataks invade Cats Lair and the Tower of Omens. Lion-O must call on the Thundercats hoping they'll stop fighting each other to defeat the Lunataks and Mumm-Ra, which they do.

After overhearing Snarf telling the Thunderkittens and Pumyra a story about Mumm-Rana's magic belt and Queen Luna (Luna's grandmother), Luna and Amuk journey to the white pyramid and take Mumm-Rana's belt, destroying her pyramid in the process. Pumyra tries to stop her but she gets sealed up in the pyramid. Amuk becomes jealous when Luna no longer needs him and during his ""little temper"", he accidently frees Pumyra. Then Luna forces Slithe and Monkian to help her ambush Lion-O and Panthro. During the battle with ""Princess"" Luna, Lion-O uses the sword to restore Mumm-Rana and she retakes the belt and defeats Luna. Amuk later arrives and destroys the belt.

Hatchiman rescues an old woman not knowing it's Luna. She "invites" him to her "cave" and there she and Chilla and Aluro attack him and take his sword, the Thundercutter. The Thunderkittens find Hatchiman and rescue him. The Lunataks plan to use the Thundercutter with their new samurai robot, Automaton, to fight Lion-O and the Sword of Omens. The Thundercutter can't tell who's good and who's evil in the fight but when Hatchiman touches the sword, the Thundercutter destroys the robot.

Bored and feeling that they are no longer needed, the Thunderkittens run away from home, but soon run into problems when they become ill from berries they had picked. A creature known as Cudi saves their lives. When the other Thundercats find them, the Thunderkittens invite Cudi to Cats Lair. But Mumm-Ra has been observing the situation and disguises himself as Cudi to gain entrance to the Lair. Many disasters occur and the blame is put on the false Cudi, who traps the Thundercats in the council chamber. The Thundercats realize it's Mumm-Ra and they manage to escape and defeat him.

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.

While trying to figure out a way to read the Book of Omens, Lion-O tries looking through the sword at the book. He is immediately drawn into the book, where a voice asks him if he has ""the key."" Lion-O says he doesn't, and four dragon heads appear and shoot fire at him. Snarf, who saw Lion-O get sucked into the book, tries to show Cheetara what happened, and he too gets sucked in. Mumm-Ra, who also watched Lion-O get sucked in, goes to cats lair and takes the book so he can destroy it with Lion-O inside. Meanwhile, just by coincidence, Panthro finds an odd looking key on Thundera. He and Tygra head back to Third Earth with the key, not knowing what it's for. Back on Third Earth, Mumm-Ra is just about to boil the book when Lion-O calls for the sword, and it brings him and Snarf back outside. Mumm-Ra takes the sword and looks through it at the book, and he gets sucked in! But Lion-O has to save him because of the code of Thundera, and Lion-O does save him. Panthro and Tygra arrive with t

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...

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

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

Vultureman creates a device that plays around with Cheetara's sixth sense. She begins to see images that aren't real, and she soon begins to lose faith in herself. Meanwhile, the Lunataks enslave Panthro with a mind control device, and tell him to make the Sky-Tomb able to fly to Thundera. When the Thundercats are looking for Panthro, Vultureman makes Cheetara see images of him being captured by Mumm-Ra, being stuck on Hook Mt., and being held at Castle Plundarr. Lion-O goes to Mumm-Ra's pyramid, and is ambushed by Luna and Amok, who capture him. Tygra goes to Plundarr and is captured by Red Eye. The Thunderkittens also get captured on Hook Mountain. Cheetara is about to go crazy, but Lynx-O tells her to listen to her heart instead of her mind. She turns into a huge ball of energy that shoots out and destroys Vultureman's device and frees Panthro and the other Thundercats.

Mumm-Ra discovers the power of one of the pieces of the treasure of Thundera. The Double-Headed Dragon of Doom, or the Jade Dragon possess the power to entrap people in its stomach. The legend says that Haji-Man's ancestor gave the dragon to his wife as a marriage gift, and since her father was so against their marriage, he put a curse on the dragon and it engulfed Haji-man's ancestor. Jaga freed the him, and he gave the dragon to Jaga for safe keeping. Now, the Thundercats have found the Jade Dragon, and Mumm-Ra manages to trap Lion-O and Cheetara in it. Haji-man is their only hope.

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...

Jaguara cannot work New Thundera’s Gyro on her own. The Thundercats order a robot to aid her in running the Gyro. Screw Loose, a robot who specializes in Gyro’s, comes to New Thundera. Mumm-Ra manages to mess up Screw Looses brain so he becomes destructive instead of helpful. The Thundercats must help Jagara get Screw Loose under control, before the entire planet is destroyed.

Tygra, on a solo trip to New Thundera to meet the other Thundercats, decides to take a shortcut through a meteor shower. His ship is damaged, and he lands on an unexplored region of New Thundera. The Moss-Land. It turns out that the moss in moss-land is part of a giant monster who captures Tygra with its moss. Lion-O and Panthro set out to save Tygra and battle the Moss Monster.

New Thundera is being torn apart and the Thundercats must present certain artifacts at various dangerous locations that used to be beautiful places, then Lion-O must go into the book and give the Key of Thundera to the guardian of the book ""at the 24th hour,"" or the Thundercats will be frozen in time and New Thundera will be destroyed. But Mumm-Ra steals the book and key and journeys into the book himself. He wants to save New Thundera BUT wants the Thundercats frozen in time. The Ancient Spirits of Evil try to stop Mumm-Ra because they fear if Mumm-Ra goes into the book, their powers will cease to exist. The other Thundercats run into problems also at the locations they are supposed to be at. Lion-O goes into the book using the Sword of Omens and battles Mumm-Ra one on one, neither of them using any magic. Even when Mumm-Ra cheats, Lion-O still wins. The ASOE summon their ""champion,"" Pyron, to then fight Lion-O, but Lion-O gets the dragons in the book to fry him... He presents the key

Recurring nightmares of Thunderians killed on Thundera as he fled to safety with Jaga and the other ThunderCats awaken Lion-O. Jaga comes to tell him that they in fact survived and are living on Third Earth. After meeting with the other ThunderCats, they decide to begin searching for them but Mumm-Ra has plans as well.

Mumm-Ra tells Aluro that the Egora Talisman will give whoever possesses it the power of extreme self-confidence. Aluro finds the talisman and uses it, along with his own powers of hypnotism, to "take away" the Thundercats' self-confidence, leaving them hopeless and confused. Only Snarf remains and it is up to him to defeat Aluro and restore the Thundercats.