Lion-O struggles with his destiny to become the next King of Thundera, as chosen by the Sword of Omens. Meanwhile, festivities are held to celebrate General Grune's return to the Cat Kingdom.
An unforeseen betrayal by a former comrade brings destruction upon the Cat Kingdom. While King Claudus leads the fight against General Slithe and his lizard army, the evil sorcerer Mumm-Ra attempts to seize the Sword of Omens.
After escaping their destroyed city with the Sword of Omens, the team encounters the Fishmen, who sail the quicksand sea in search of a massive sea creature. The ThunderCats’ quest is to find the Book of Omens … but Lion-O is more interested in revenge on Mumm-Ra.
While traveling through the woods, the ThunderCats come across a group of Petalars - small plant-like creatures whose lifespans are only one day. Lion-O befriends the young Emrick as he and the others try to figure out a way out of the woods and return the Petalars to their home. Meanwhile, Slithe and his lizard army are hot on the ThunderCats' trail to eliminate them.
The ThunderCats accompany Panthro to Cloud Peak Mine to search for Thundrilium for the Thundertank. Along the way, Panthro and Grune's past is explored, from their first encounter to the reason behind Grune's betrayal.
The ThunderCats continue their quest for the Book of Omens, which leads them to the fabled Tower of Omens. However, they will first have to get past a series of deadly traps in order to reach it. Meanwhile, Mumm-Ra grows tired of waiting and forces Jaga to reveal the Book's location, and plans to go there himself to take it at all costs.
Lion-O's soul is transported into the Book of Omens and he sees what life was like in the eyes of his ancestors as they start a rebellion against Mumm-Ra and discovers the origins of the Sword of Omens and the Warstone, which takes on the familiar shape of the Eye of Thundera during the course of events Lion-O is made to experience in his ancestor's body. Lion-O also learns from Jaga that in order to defeat Mumm-Ra, he must first find the remaining three Warstones that are scathered on Third Earth and unify the rest of the animals to create an army.
As Tygra and Panthro work on the ThunderTank, Lion-O is searching for supplies and encounters a mysterious Drifter who helps teach a few important lessons. After showing off The Sword of Omens in town, Lion-O is challenged by a man known as The Duelist and must overcome himself in order to win.
The ThunderCats meet the mysterious beings who had helped them during the night and they turn out to be the Berbils, or Ro-Bears. The Berbils treat the ThunderCats with great hospitality until the village is attacked and some of the Berbils are captured. The ThunderCats help their new friends and a battle for freedom ensues.
The Cats track the location of the first stone to the mystical Elephant Village, but Lion-O can't find the specific location and the forgetful Elephants no longer remember where it is.
When in the Forest of Magi Oar, the ThunderCats send WilyKit, WilyKat and Snarf to search for firewood. After they return, they start a fire and lay down to rest. Lion-O then throws a special piece of firewood that releases several seemingly evil spirits around them. After Lion-O and the rest of the ThunderCats cannot defeat them, the ThunderCats meet the Wood Forgers who have a talent for using paper magic in combat.
Tygra's jealousy boils over, leading to a clash with Lion-O.
While Lion-O and Tygra are in the Astral Plane dealing with their issues which have been magnified by the powers of Mumm-Ra who wants them to destroy each other, the other Thundercats protect the village from Slithe, Grune and the Lizard army. The Elephants make a surprising decision after meditating and Lion-O realizes the truth of being betrayed by Tygra. Panthro has some interesting flashbacks while telling Wily Kit and Wily Kat how Grune lost his tooth, and in the end Panthro makes a sacrifice to defeat his enemy.
The Thundercats go on the offensive taking down Mumm-Ra’s lizard army piece by piece. Lion-O appeals to the soldiers to turn against their overlord, but Mumm-Ra won’t see his army crushed so easily. He tasks Slithe with recruiting two new and vicious Generals — Addicus and Kaynar — to retaliate against the cats. Meanwhile, the Robear Berbils make Panthro a new set of robotic arms and soop up the Thundertank.
The ThunderCats are ambushed by Slithe who is now assisted by Kaynar and Addicus. When Lion-O is knocked into the river and pinned down by the rocks, he finds himself in the spirit world where Jaga tells him that he must pass a bunch of tests in order to return to the living. The first test taking place in the simulation of Thundera's slums has Lion-O trying to figure out which Wilykit and Wilykat has the key to pass to the next test. The second test has Lion-O having to race Cheetara through a labyrinth. Back in the living, Tygra and the other ThunderCats managed to get free from their shackles, but Slithe, Kaynar, and Addicus escape with the Sword of Omens. Tygra vows to get the Sword of Omens back.
Lion-O must finish his trials in order to rescue the other ThunderCats from Mumm-Ra and his army.
While traveling through snowy mountains in search of safe passage, Tygra and Lion-O come upon a lost tiger village and in it they find Tygra's real father. Tygra learns why his father sent him away as a baby — to save his life. But all is not as it seems in this village as the brothers learn these tigers are cursed and Tygra may be the answer to saving them — but at the cost of his own life.
While Lion-O and Tygra were off with the tiger clan adventure, the rest of the crew is keeping an eye on the Thundertank. The twins are looking for some stashed food, but it appears Snarf beat them to the goodies. Panthro and Cheetara decide to use this as an opportunity to teach these two how to survive on their own.
A refugee cat is forced to fight in gladiator-style battles in a city of dogs.
Arriving at Mount Plun-Darr, the ThunderCats and Pumyra discover that the Thunderian slaves are being forced to excavate the Sword of Plun-Darr for Ratar-O and his Rats.
Mumm-Ra arrives at Mount Plun-Darr and battles the Thundercats in an attempt to regain the Sword of Plun-Darr.
WilyKit, WilyKat, and Snarf track down a thief in Dog City.
The Thundercats require the assistance of a snake oil salesman named Ponzie to defeat Mumm-ra’s latest monstrous form.
After making it back to the City of Dogs, Panthro is wondering why the Book of Omens is pointing to the sky. Lion-O runs into Jorma who had survived the attack on Thundera and has made it home. Upon studying the book, Jorma concludes that one of the stones the ThunderCats are after is somewhere in the sky. While exploring a secret scrap pile where new scrap metal falls from the sky, Lion-O, Tygra, Panthro, and Jorma are attacked by Necromech robots which end up stealing the Book of Omens. Upon tracking the Necromech robots, Lion-O, Tygra, and Panthro discover that they work for the Soul Sever (an alien turned robot by the Necromechs) who plans to use the power of the Book of Omens in order to find vessels for the three spirits of his deceased family.
The book of Omens leads the Thundercats to a city in the sky ruled by birds!
The ThunderCats must stop Mumm-Ra from getting the Tech Stone!
Snarf is in charge of watching Baby Lion-O. When a butterfly catches Baby Lion-O's attention, he follows it through town, narrowly avoiding disaster along the way. Snarf does his best to catch up with and save Baby Lion-O, but ends up suffering the consequences that Baby Lion-O escapes. At the end of the day, when Snarf believes he failed by losing Baby Lion-O, the butterfly returns, along with Baby Lion-O. King Claudus congratulates Snarf on a job well done and appoints him as Baby Lion-O's personal caretaker. As Snarf prepares Baby Lion-O for bed, several butterflies appear, much to Baby Lion-O's delight, and to Snarf's chagrin.
