Lion-O, always outdone by his adoptive older brother Tygra, undergoes the ritual to be chosen by the Sword of Omens as the next king of Thundera. His father, Claudus, does not feel his son is ready because he is too lenient and easily distracted by flights of fancy like the myth of ancient technology. Soon after, King Claudus welcomes the return of his friend Grune and holds a celebration in both his honor and in memory of the fallen Panthro. During the event, Lion-O defends a pair of captured Lizards and convinces his father to release them.

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.

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 ventures into the Book of Omens where he becomes the incarnation of his renowned ancestor, the valiant Leo, who led the rebellion against Mumm-Ra in a previous millennium.

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.

Sent by the Elephants to the Forest of Magi Oar, Lion-O must learn to master Sight Beyond Sight before returning to the Elephant Village. The Cats encounter a group of paper warriors with a dark secret.

The Cats are ready to retrieve the stone from the "Astral Plane" in the Elephant Village, but find it overtaken by Grunea and Mumm-Ra's forces. Plus, Tygra and Cheetara's early relationship to one another is revealed.

Tygra and Lion-O enter the Astral Plane to retrieve the stone, but encounter Mumm-Ra in the process. Grune and Panthro have their final duel. Cheetara finally chooses her beau.

The ThunderCats go on the offensive, but Mumm-Ra won't see his lizard army crushed so easily. He tasks Slithe with recruiting two new and vicious Generals.

During an ambush, Lion-O falls to his death, but he is given a second chance at life - if he can pass a series of trials that pit him against each of his teammates.

Pleading for a chance to save his friends, Jaga grants Lion-O life until sunrise to try and save his friends ... and stop Mumm-Ra.

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.

The Thundercats discover a cat refugee, Pumyra, being forced to fight as a gladiator 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.

Seduced by the fun-loving lifestyle of Tookit and the orphans they meet, WilyKit and WilyKat are tricked by Tookit into becoming thieves again.

The Thundercats require the assistance of a snake oil salesman named Ponzie to defeat Mumm-ra’s latest monstrous form.

While trying to uncover the location of the next stone, the ThunderCats cross paths with a mad man, Soul Sever, who is trying to insert the souls of his long-lost family into machines.

The ThunderCats' search for the Tech Stone leads them high above Thundera to the floating bird city of Avista, where the stone is the power source for their city.

In the season finale, Mumm-Ra's forces find the ThunderCats and the Tech Stone in Avista City. An incredible battle ensues for the stone as Lion-O finds himself betrayed by a trusted ally.