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.

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.

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 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.