Lion-O has nightmares of Thunderian countrymen who were left behind on Thundera while he and the other ThunderCats escaped. Jaga tells Lion-O that the Thunderians survived Thundera's destruction after being rescued by space-traveling Berbils and that they are alive and well on a deserted island somewhere on Third Earth. Lion-O and the ThunderCats set out to find the Thunderians, but so does Mumm-Ra and his followers.
Under Mumm-Ra's orders the reformed Berserkers capture the Thundarians. Lion-O's rescue attempt fails and the captured Thunderians are taken to Fire Rock Mountain after another failed attempt on their part to break free from their captors. The group is eventually place in a prsion cell at Fire Rock Mountain.
While trying to get up the mountain, Lion-O loses the Sword of Omens in an avalanche. While Panthro battles the Fist-Pounder with the ThunderTank. The Mutants arrive at Fire Rock Mountain to take control of the prisoners. The Thunderians attempt to escape their prison. Lion-O arrives at the mountain and is confronted by Hachiman who believes (thanks to Mumm-Ra's evil magic) that Lion-O is causing the suffering of his ancestor.
After Lion-O is nearly killed, Hachiman is able to break free of Mumm-Ra's spell, he and Lion-O are reconciled and the ThunderCats close in on rescuing the Thunderians from Fire Rock Mountain. But then Mumm-Ra himself makes an appearance to try and defeat the Cats. Jaga then arrives with some much needed supernatural help in the form of Star of Thundera after the Star helps him defeat Grune the Destroyer. Mumm-Ra manages to take the Star from Jaga but to no avail. When he tries to use its powers himself, it instead attacks and seeminlgy destroys him.
- Thunderians; Lynx-O, Bengali & Pumyra
- Berserkers; Hammerhand, Cruncher, Ram Bam & Top Spinner
- Mutants; Slithe, Monkian & Jackalman
- Snowman & Snowmeow
- Berbils; Ro-Bear Bert & Bob
- Mutants: Ratar-O & Vultureman
- Grune the Destroyer
- Turmagar, Tuska Warriors, Gomplin
- Captain Shiner & crew
- When the Berserkers storm the island on which the three Thunderians and Berbils live, there is an extensive fight scene, showing the Thunderians and Berbils manning self made defensive weapons. Most of these scenes are missing in the VHS release.
- While Snowman nurses Lion-O, they are spotted by Slithe, who goes in for a closer look. Deleted from the VHS version is an extended conversation between the mutants on what course of action to take. Slithe wants to attack, but Monkian and Jackalman aren't sure whether it's wise to go against Mumm-Ra's orders.
- Before Lion-O is chased by the Fist Pounder, there is a deleted confrontation with Snowman. It is this brief encounter that explains how the end of Snowman's lance comes to be broken.
- After Panthro leaves Hook Mountain in the Thundertank, there is a scenes not present on the VHS. Jackalman and Slithe eat while Monkian gets the Fistpounder into position to wait for Panthro. The Thunderians overhear this and are resolute to escape.
- When Lion-O tries to enter Mumm-Ra's Pyramid, he encounters Ma-Mutt for the first time. Those scenes did not make the cut for the VHS.
- The Berzerkers argue over who gets the biggest share of Mumm-Ra's gold. This scene did not make the cut for the VHS.
- Due to the removal of commercial breaks and credits, several cliff-hanger freeze-frame shots where not seen on the VHS.
- In the UK, as with the rest of the series, Panthro's use of nuchuks was heavily edited. Unlike the the rest of the series, the shot of Panthro doing so during the credits was cut completely instead of being substituted for a shot with no weapon. As a result, the VHS version has an abrupt jump during the theme song.