The Thundercats depart Third Earth for New Thundera, leaving Tygra and Pumyra behind to watch over the Cat's Lair and Tower of Omens. Meanwhile, the Ancient Spirits of Evil resurrect Mumm-ra, building a new pyramid on New Thundera.
More and more earthquakes are occurring on New Thundera thanks to Mumm-Ra's sabotage of an arcane machine that lies at the center of the planet that holds its gravity together, watched over by the ancient Thunderian sorceress, Jagara.
The Ancient Spirits of Evil bring a creature to Mumm-Ra called a Mirror Wraith, which he transforms as a doll and gives to a lost thunderian child named Leah, who keeps it and unwittingly puts the Thundercats in great danger.
While exploring New Thundera, Wilykit and Wilykat stumble upon a mysterious orb of gold and pick it up, believing it to be one of the Treasures of Thundera. However, it soon transpires that that is not the case.
Jagara cannot work the new Gyroscope alone, so the Thundercats send for someone to aid her. Screwloose, a robot who specializes in the technology, comes to Third Earth. But, Mumm-Ra tampers with his programming, making him destructive.
Mumm-Ra resurrects the ancient alchemist Malcar, but he returns old and weak. Mumm-Ra then sends him to the Canyons of Youth, which will restore his youth and power so that he may effectively defeat the Thundercats.
Mumm-Ra has a powerful device called the Babylonian Babarian Boiler, that he plans to use against the Thundercats. However, the bumbling Ma-Mutt accidentally destroys the machine, causing an enraged Mumm-Ra to banish him from the pyramid.
The Ancient Spirits of Evil unleash the Shadowmaster, a dark sorcerer who may be even more powerful than Mumm-Ra. Fearing the Sprits will favour the Shadowmaster over him, Mumm-Ra hatches a secret plot to aid his enemies the Thundercats.
An ecology inspector comes to New Thundera to inspect the new Cat's Lair. His ship uses the Space Way Airborn Navigation system to direct him to planets throughout the universe. Upon arriving he is ambushed by Two-Time, who steals the ship.
Vultureman escapes the Circus Train by hijacking a bookmobile. He discovers information about a powerful enemy of Mumm-Ra, Zaxx. Using this knowledge, Vultureman plots to overthrow Mumm-Ra and rule the universe.
The key to the Book of Omens is finally solved and it is unlocked. All of the team must pass different tests to save the planet, and Lion-O faces many trials within the book to prove himself once and for all as Lord of the Thundercats.