Recurring nightmares of Thunderians killed on Thundera as he fled to safety with Jaga and the other ThunderCats awaken Lion-O. Jaga comes to tell him that they in fact survived and are living on Third Earth. After meeting with the other ThunderCats, they decide to begin searching for them but Mumm-Ra has plans as well.

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.

Lion-O loses the Sword of Omens in an avalanche. 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 Fire Rock Mountain and is confronted by Hachiman who believes Lion-O is causing the suffering of his ancestor.

Lion-O and Hachiman are reconciled and the ThunderCats close in on rescuing the Thunderians from Fire Rock Mountain. But they'll need supernatural help if they are to pass through the Thundranium gases to reach them.

Mumm-Ra is weak and faces the threat of three new ThunderCats; he sends the Mutants to release his old enemies, the Lunatacs, imprisoned in Dark Side[29] in order to bolster the forces of evil. The ThunderCats' celebration of their victory over Mumm-Ra and the welcoming of three new ThunderCats is cut short when Snarf overhears plans at Castle Plun-darr after he chased Ma-Mutt there from the Berbil village.

The Mutants succeed in releasing the Lunatacs. The ThunderCats discover their Thundrylium mine is being looted and people are being kidnapped from the villages. Lion-O & the ThunderKittens have their first run-in with a Lunatac and Bengali's skills as a blacksmith come in handy.

The ThunderCats build the Tower of Omens to monitor for Sky Tomb, which will be run by the new ThunderCats. Disguised as a Berbil, Ma-Mutt spies on the ThunderCats' plans and the Lunatacs are sent to destroy the Tower. Snarfer contacts Snarf to tell his uncle that he's returning to Third Earth.

Mumm-Ra's power is restored. Snarfer makes it to Third Earth, but crashes in Dark Side. The ThunderCats rush to his aid before the Lunatacs can get a hold of him.

The ThunderCats look for Sky Tomb to free the slaves imprisoned inside it. Bengali must learn the importance of teamwork as Lion-O leaves him with guard duty. Lynx-O and Cheetara run reconnaissance to find out if Mumm-Ra is truly back or not.

By disguising himself as Jaga, Mumm-Ra tricks Lion-O into believing the new ThunderCats are traitors so that they will fight amongst themselves.

Mumm-Ra tells Alluro where to find a talisman that boosts the self-confidence of the one who possesses it so that they become nearly invincible. Snarf learns that true courage comes from within.

Ma-Mutt digs up an ancient book, which leads Mumm-Ra to search for the ancient evil of the mask of Gorgon

The Lunatacs look for Thundrylium in a cave on Hook Mountain, only to be driven mad by a strange creature that turns them against each other.

Mumm-Ra coats the Bezerker's weapons and armor with Thundranium. Wilykit and Wilykat find that guarding Cats' Lair is not always a breeze.

Mumm-Ra activates a mesmerizing beacon on Ravage Island, which draws the ThunderCats to it and takes hold of their minds.

While taking care of a dangerous Suspension Capsule, dug up near Cats' Lair, Lion-O is exposed to harmful gasses inside that cause him grow younger. If the ThunderCats do not find a solution in time, he will rapidly become younger until non-existent.

Vultureman builds a sonic gun from a sound stone he stole in Dark Side as the Lunatacs join with him to attack the Tower of Omens.

The day of the centennial total eclipse has arrived, and any spell Mumm-Ra casts will last until the next eclipse. He declares a "Day of Decay" on the Cats' Lair, causing it to fall apart.

Chilla freezes Snarfer's spaceship as he heads back to the Tower of Omens with Berbil Mexican takeout. When Mandora gets involved, Chilla freezes her and becomes a fugitive from the law as Mandora sets her sights on bringing her in.

Luna discovers that her grandmother's magic belt is now in the possession of Mumm-Rana, who claimed it after battle. She heads straight for the white pyramid, with Pumyra hot on her tail.

While Hachiman is on his way to the Tower of Omens, Luna steals his sword, the ThunderCutter, and gives it to an automaton. Lion-O and the ThunderKittens head out to find their old friend.

Fed up of feeling useless, Wilykat convinces his twin to run away from home, but living on their own is more dangerous than they realized. The other ThunderCats search desperately to find them as they all must learn a lesson in communication.

While all the ThunderCats except Lion-O are gone, Mumm-Ra switches Ma-Mutt with Snarf. Ma-Mutt poisons Lion-O, allowing Mumm-Ra to move in.

Vultureman builds a Thundranium[28] projector, capable of creating concentrated regions of Thundranium. When the ThunderKittens damage it, he damages their spaceboard, sending them off into danger. While Lion-O and Snarf search desperately for them, Vultureman plans his revenge.