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.

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.

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.

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.

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.

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.