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.

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.

Mumm-ra finds the Totem of Dera (a part of the T-cat treasure) which has special healing powers and can bring inanimate objects to life. He gives it to Vulture-Man and the Mutants so they can make a device to destroy the T-cats. After making the device, the mutants decide to test it near a swamp. At Cat's Lair, Lion-O sees that there is some mutant activity near the swamp. He, Wilykit, and Snarfer decide to check it out. When going to the swamp, the Hovercat is brought down by a swamp monster made by the device. The Hovercat crashes in the swamp, and Lion-O gets intoxicated by the deadly swamp water. Jaga appears and tells Snarfer that he must get the Totem of Dera to heal Lion-O. Snarfer gets the Totem and succeeds in healing Lion-O. Lion-O calls on the T-cats to try to kill the swamp monster. When all their weapons prove ineffective against the monster, the T-Cats come up with the idea to dissolve the monster in water and they succeed in defeating it.

Panthro, Tygra, and Cheetara return to New Thundera in the Feliner to find more of the Treasure of Thundera, but Mumm-Ra shoots the Feliner down and, as the Fog of Despair, sends them to the Canyons of Youth, which changes them back into Thundercubs. Then Mumm-Ra disguises himself as Lion-O and tells the Thundercubs to find the treasure for him. Meanwhile, back on Third Earth, Lion-O and Snarf decide to go rescue the Thundercats on New Thundera, but they must ask the Mutants to take them to New Thundera in the Rat-Star. The Mutants agree, secretly planning to attack Lion-O once they're in space. They do attack and imprison him and Snarf on the way to Thundera, but they manage to break out. Cheetara meanwhile, using her sixth sense, locates part of the treasure, the Mirror of Truth. The real Lion-O shows up, and uses the Sword of Omens with the Mirror of Truth to restore the cubs to their proper age, and Mumm-Ra reveals himself and turns into Mumm-Ra the everliving. Cheetara uses the mi

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 Ancient Spirits of Evil bring the Mirror Wraith to Mumm-Ra, and he disguises it as a child's toy. Mumm-Ra then intercepts a thunderian escape pod which carries in it a little girl. He gives the toy to the child (Leah), and leaves. She is rescued by the Thundercats, and goes into New Cat's Lair with the doll. The doll turns into the Mirror Wraith when left alone, and begins to destroy Cat's Lair, and the Thundercats have no clue where the evil Mirror Wraith came from.