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.

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 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 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.

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.

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.

Two Bolkins (sheep-like beings from Third Earth) unleash the ghost of Grune the Destroyer, a renegade Thundercat who once terrorised Third Earth and now turns his attention to the Thundercats.

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.

Lion-O undergoes the fourth task in his Anointment Trial.

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.

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?

Wily Kit and Kat stand in Lion-O's way on the third day of his trials. Lion-O must beat them through the maze of infinity. Attempting to stop Lion-O and slow him down, the kids set traps in the maze. He manages however to avoid their traps. In order to beat them through the maze, Lion-O plays their own tricks on them, and tricks them into losing the race through the maze.

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

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

When a meteorite made of pure Thundrillium crashes on Hook Mountain, the Thundercats decide to use it to replenish their depleted energy supply. But Lion-O must first gain the trust of the fierce Snowman.

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.

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.