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 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.

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...

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...

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.

Capt. Cracker and his mechanical parrot Polly land on Way-Out Back and free the Lunatacs and put Bragg and Crownan in one of the train's cages. They plan to go to Third Earth to attack it since most of the Thundercats are no longer on Third Earth. Meanwhile the ThunderCats have learned Cracker escaped and Snarfer and Mandora go to catch him. Bragg has Crownan ride a fire exstiquisher, so he can get into space and get help. Mandora finds him, and the three of them go to Third Earth. Mandora fights with Cracker and the Lunatacs, but is beaten and she and Snarfer are tied to her cycle and sent towards a mountain. Lion-O, Panthro, and Cheetara arrive and Lion-O saves Mandora and the others. Meanwhile Cracker and the Lunatacs go to attack Cats Lair, only occupied by Pumyra, but Lion-O uses the Eye's signal to cause the drawbridge to tilt, sending Cracker and the Lunatacs into the moat. The Lunatacs are exiled again.

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

The Ro-Bear Berbils are a friendly group of robot bears that live on Third Earth. Lion-O and Snarf don't know this, and end up getting caught in a Ro-Bear trap. The Berbils free them however, and they form an alliance. Mumm-ra attacks the Berbil village, but the Thundercats save it. In return, the Ro-Bears help the Thundercats to build Cats' Lair, a new base for the Thundercats.

Mumm-Ra and the Mutants plot to open the Time Warp Prison and release the evil Princess Ta-She in order to use her deadly Doomgaze against the Thundercats.

Wily Kit and Kat are constructing a well for the New Cat's Lair on New Thundera. The Thundercats on New Thundera receive a distress signal from Thunderian refugees trying to find their way to New Thundera. The Kittens are left alone with Snarf on at the New Cat's Lair, and Lion-O and Snarfer are out constructing an early warning device (I guess for weather purposes). The rest of the Thundercats seek out the refugees in space. When Wily Kit and Kat strike water, they accidentally unleash a monster that Jaga trapped in the underground lake centuries ago. Frogman, with aquatic powers, tries to sink the New Cats Lair. Lion-O however re-traps Frogman in his watery prison.

Mumm-Ra summons Malcar, an ancient alchemist, to return from the dead. The alchemist returns old and weak, as he was when he died. Mumm-Ra takes him to the forest of youth to restore his youth and power. Malcar regains his powers, and uses them against the Thundercats. He transforms all the Thunderillium on the planet into Thundrainium.

From the Shadow Realm, the Shadowmaster contacts the Ancient Spirits of Evil (ASOE), telling them of how he captured Lion-O's father, Claudus, just before Thundera blew up. Then the Shadowmaster, through a bad dream, shows Lion-O his captured father and challenges Lion-O to a fight. Lion-O goes to the Shadow Realm through the Book and Sword of Omens, and is able to fight the Shadowmaster as long as the Sword stays bonded to the book. However, the Shadowmaster sends a huge bat to steal the Sword. It succeeds, and then Lion-O becomes very weak in the Shadow Realm. Mumm-Ra meanwhile, feeling like the ASOE will turn against him in favor of the Shadowmaster, sends Ma-Mutt to secretly steal the sword from the bat and put it back near the book. This renews Lion-O's strength, who calls for the Sword, rescues Claudus, and exiles the Shadowmaster. Claudus leaves Lion-O, but at the end you see him and Jaga standing next to each other in that blue, ghostly form. Now Lion-O has 2 mentors to give hi