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 controlled by the Gyroscope under the Churning Rocks at the center of the planet and will use this knowledge to destroy the Thundercats and trick the Gyroscope's guardian, the ancient sorceress Jaguara.

Return to Thundera – Pt. 2

More and more earthquakes are occurring because of the malfunctioning Gyroscope. Meanwhile Lion-O receives 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 thief who wants the Sword for himself.

Return to Thundera – Pt. 3

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.

Return to Thundera – Pt. 4

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.

Return to Thundera – Pt. 5

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.