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.

The Mutants, once again searching for a way to destroy the Thundercats, recover some more items from their spaceship. They take their ship's engine and convert it into a giant fireball-shooting machine. The mutants terrorize Third Earth with their fireballs, until the Thundercats go to castle Plunn-Darr and destroy their dangerous new weapon.

Mumm-Ra tricks Lion-O into using the Sword of Omens against Tygra, causing the blade to break in half and lose its powers. The only way Lion-O can restore the Sword is to venture into a volcano and have the Inflamer reforge it. But the Inflamer requires a payment of gold... Has Lion-O taken on more than he can handle?

An evil hunter lands on third earth in search of prey to hunt. His holographic machine can tell him about all of the Thundercats, including their strengths and weaknesses, and he is able to hunt down each one of them and put them in Thundrainium cells. He captures all of them but Lion-O and Snarf. Jaga warns Lion-O about Safari Joe before he sets out to save his comrades, and Lion-O is able to defeat him and release his friends.

Vultureman invents a Super Power Potion which give him magical powers, enabling him to mesmerize and defeat Tygra.

Jackalman ambushes Snark and attempts to steal the Sword of Omens. This gives Panthro the idea to make a duplicate sword as bait for the Mutants.

Mumm-Ra creates a museum where painting and statues come alive to oppose the ThunderCats.

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.

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

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...

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.

Mumm-Ra plans on using the legendary Mask of Gargon to free a sleeping child in the hills of Elfshima to use against the Thundercats. When Chilla and Tug Mug fail to get the mask because it turned them to stone, Mumm-Ra summons it and decides he needs the Eye of Thundera so that the mask can use sight beyond sight to awaken the giant child. Lynx-O warns the Thundercats of the mask and the sleeping child, but Lion-O, Panthro, and Willa still go to the pyramid, but are turned to stone by the mask. Mumm-Ra then uses the Eye of Thundera and the mask to awaken the giant. But Lynx-O and Ben-Gali in the Thunderstrike defeat the giant and the mask gets smashed apart restoring everyone who had been turned to stone, and the Eye of Thundera burns the book that contained the mask's terrible secrets.

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...