ThunderCats follows the adventures of the eponymous team of heroes, cat-like humanoid aliens from the planet of Thundera. The series pilot begins with the dying Thundera meeting its end, forcing the ThunderCats (a sort of Thunderean nobility) to flee their homeworld. The fleet is attacked by the Thundereans's enemies, the Mutants of Plun-Darr, who destroy all the starships in the "ThunderFleet," but spare the flagship hoping to capture the legendary Sword of Omens they believe is onboard. The sword holds the mystical Eye of Thundera, the source of the ThunderCats's power, embedded in the hilt. Though the Mutants damage the flagship, the power of the Eye drives them back, and Lion-O's elderly guardian, Jaga, pilots the ship to the safety of the world of "Third Earth"; however, he dies in the process, as there are insufficient cryo-stasis pods aboard the ship, and the journey to Third Earth takes several decades even with advanced interstellar spacecraft. The flagship contains the young Lord of the ThunderCats, Lion-O, as well as the ThunderCats Cheetara, Panthro, Tygra, WilyKit and WilyKat, and Snarf.
When the ThunderCats awake from their suspended animation on Third Earth, Lion-O discovers that his suspension capsule has failed to inhibit his aging, and he is now a child in the body of a man. Together, the ThunderCats and the friendly natives of Third Earth construct the "Cat's Lair," their new home and headquarters, but before long, the Mutants have tracked them down to Third Earth. The intrusion of these two alien races upon the world does not go unnoticed, however - the demonic, mummified sorcerer, Mumm-Ra, recruits the Mutants to aid him in his campaign to acquire the Eye of Thundera and destroy the ThunderCats so that his evil might continue to hold sway over Third Earth.