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.

The Mossland Monster

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.

Ma-Mutt’s Confusion

Mumm-Ra has a new device, the Babylonian Barbarian Boiler, that he plans to use on Cats Lair. Ma-Mutt fools around too much and Mumm-Ra banishes him from the Pyramid. Later, the Thunderkittens, Snarf, and Snarfer bring Ma-Mutt back to Cats Lair and then Mumm-Ra fires the Boiler's beam at the Lair, which causes it to start melting. Snarfer makes a communicating device (because Ma-Mutt was trying to tell them about the beam), so they can understand Ma-Mutt. Ma-Mutt starts telling them of the Boiler, but Mumm-Ra sees this and through the Cauldron's magic brings Ma-Mutt back to the Pyramid.

The Shadowmaster

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 will be crucial to Lion-O's triumph in this realm.

Swan Song

An Ecology Inspector (EI) comes to Thundera to inspect the new Cats Lair. His ship uses the SWAN system (Space Way Airborn Navigations) to direct him to planets all over the universe. When he arrives on Thundera, he gets ambushed by Two-Time. Two-Time uses a hologram to make the EI's ship crash into a mountain, and then when the Thundercats come to rescue the EI in the Feliner, Two-Time uses the hologram again. Lion-O manages to fly around the mountain and lands the Feliner. Meanwhile, Two-Time flies to new Cats Lair in his spaceship, Dome-Down. He actually picks up the whole Lair and keeps it inside Dome-Down.

The Touch of Amortus

Mumm-Ra orders Amortus, a being he banished to the Land of No Return centuries ago, to destroy Lynx-O. Amortus makes Lynx-O crash in the Thunderstrike, and then he touches Lynx-O's face. The spell from the touch makes Lynx-O feel like he is an outcast, so he leaves to join Amortus in the Land of No Return. The other TCats, Lion-O, Panthro, and Cheetara, go after him. In the Land of No Return, Amortus again touches Lynx-O, this time causing him to turn to stone. The other TCats arrive and try to beat Amortus, but he touches all of them, causing them to start turning to stone. But just as Lion-O is about to turn entirely to stone, he calls the Sword and it breaks them free.