The Thundercats think that they have destroyed Mumm-Ra for good. Little do they know that he survived. He returns to his tomb with the help of Ma-Mutt, and is to weak to do anything. So he transforms Ma-Mutt into an image of himself, and sends this image to order the mutants to release the Luna-tacks.
The Luna-tacks have been freed by the mutants. Mumm-Ra joins forces with them to destroy the Thundercats, and after doing so, they would rule third earth together. The Luna-tacks meet the Thundercats in battle, and prove to be much stronger than them. In fact, Tugg-Mugg, one of the Luna-tacks manages to break the sword of omens in half. Bengali however manages to reforge it since he is a Thundarian Blacksmith.
The Luna-tacks build their fortress with the help of the brute men. They call it Sky-Tomb, and not only is it powerful, but it can travel through the air. It is a mobile fortress. The Thundercats ask the Berbils to help them build a new structure called the Tower of Omens, that would help them easily locate the position of Sky Tomb, and stop the Luna-tacks as fast as possible.
Young Snarfer, Snarfs nephew, arives on third earth. His ship has gone off course though and landed in territory of the Luna-tacks. The Luna-tacks manage to capture Snarfer, and the Thundercats must venture into Darkside to save young Snarfer so he can work the Tower of Omens.
Lion-O, Panthro, Tygra, and Pumyra set out to Darkside to free the slaves the Luna-tacks have imprisoned. In doing so, they get captured. Cheetara and Lynxo set out to Sky Tomb to save them. The Thundercats see Mumm-Ra for the first after his ""death"" time at Sky Tomb, and discover that he cannot be harmed by his own reflection anymore. The ancient spirits of evil have made him more powerful when they revived him. They Thundercats manage to escape, and leave the Luna-tacks fighting amongst themselves.
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.
Mumm-Ra tells Aluro that the Egora Talisman will give whoever possesses it the power of extreme self-confidence. Aluro finds the talisman and uses it, along with his own powers of hypnotism, to "take away" the Thundercats' self-confidence, leaving them hopeless and confused. Only Snarf remains and it is up to him to defeat Aluro and restore the Thundercats.
Mumm-Ra plans on using the legendary Mask of Gargon to free a sleeping child in the hills of Elfshima to use against the Thundercats. When Chilla and Tug Mug fail to get the mask because it turned them to stone, Mumm-Ra summons it and decides he needs the Eye of Thundera so that the mask can use sight beyond sight to awaken the giant child. Lynx-O warns the Thundercats of the mask and the sleeping child, but Lion-O, Panthro, and Willa still go to the pyramid, but are turned to stone by the mask. Mumm-Ra then uses the Eye of Thundera and the mask to awaken the giant. But Lynx-O and Ben-Gali in the Thunderstrike defeat the giant and the mask gets smashed apart restoring everyone who had been turned to stone, and the Eye of Thundera burns the book that contained the mask's terrible secrets.
The Madd Bubbler, an ancient creature of third earth who lives in an old Thundrilium mine on hook mountain has the power to turn all creatures into evil beings, and making people accept his modo - "destroy, or be destroyed". He manages to seduce the Luna-tacs to fight against each other, and afterwards Panthro, Tygra, and Cheetarah. They fall under the bubblers power and begin fighting each other to the death. Lion-O, observing these occurrences through the sword of omens finds out from Jaga that snarfs are not capable of evil. He summons Snarf and Snarfer and tell them to retrieve the Thundercats from the mine so that they can be returned to their normal selves.
Mumm-Ra summons the Berserkers and coats their armor with Thundrainium and sends them to attack the Thundercats at the Tower of Omens. Realizing that their armor is coated with Thundrainium, the Thundercats at the tower need help and Lion-O and Tygra rescue them. They create a windstorm to rub off the Thundrainium and the Berserkers retreat. Meanwhile the Lunataks invade Cats' Lair and the Thundercats must rush back to save the Thunderkittens and Snarf who are being held as the Lunataks' slaves.
Mumm-Ra uses the Beacon of Ravage Island to make the Thundercats his slaves. When the beacon puts Lion-O, Panthro, Cheetara, and Pumyra under its power, they are easily captured by the Mutants, and Snarf must get the others at the tower for help, but Ben-Gali soon falls under the beacon's power and it's up to Lynx-O, Snarf and Snarfer, to save the "enslaved" Thundercats.
While burying one of the time capsules that transported the Thundercats to Third Earth, it smashes apart and Lion-O gets caught in its gases, making him younger and younger by the minute. The other Thundercats must find a way to reverse the process and realize the Cave of Time is the only way, but they must get Lion-O there before he "vanishes" from existence. Things get worse when the young Lion-O and Snarf are captured by the Lunataks.
Vultureman develops a sonic gun to destroy the Thundercats. Since the other Mutants refuse to help, Vultureman decides to go on his own until the Lunataks ""kidnap"" him and force him to help them. Vultureman uses a legendary sound stone to power the device and he and the Lunataks use it against the Thundercats at the Tower of Omens. The Thundercats barely escape and are saved by Lion-O, but they lose the tower to the Lunataks. The Thundercats must design a sound weapon of their own with a sound stone to counter Vultureman's weapon and retake the Tower of Omens.
Third Earth is experiencing a total lunar eclipse and Mumm-Ra uses this eclipse to cast a spell that will cause Cats Lair and everything in it to malfunction. The Thundercats first notice this when things start falling apart and fail. Lion-O and Panthro must fight the Mutants while having problems running the Thundertank. They still manage to defeat the Mutants, but crash the Thundertank. Lion-O realizes that this must be Mumm-Ra's evil work and goes to the pyramid to stop Mumm-Ra. Meanwhile Cats Lair is getting worse as Cheetara and Tygra rush to fix things in the lair but are attacked by the Lunataks. They defeat the Lunataks temporarily, but the Lunataks return to finish off the Lair. In order to break the spell, Lion-O must use the Sword to block out the sun
Snarfer is making a trip back to Third Earth bringing food for the Thundercats, but he gets sideswiped by Chilla. Mandora, evil chaser sees this and pulls Chilla over. Chilla, however, ices Mandora and makes a run for it. Mandora insists on the Thundercats' help to capture Chilla. But when she and Lynx-O go to Darkside to capture Chilla, they fall into one of the Lunataks' traps. It seems that the Lunataks wanted the Braille board so that the Thundercats could not get to them. But when the board disappears, they try to get the information from Lynx-O as to where it went, but Mandora escapes and frees Lynx-O. She is tricked however and she and Lynx-O are shot up into space in a pod. Lion-O brings them down by using the Sword, and they return to Darkside and Mandora succeeds in capturing Chilla.
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.
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.