Amortus, an evil tentacled creature banished eons ago by the Thunderians, has returned to the new ThunDERa through Mumm-Ra's cauldron.
The ThunderCats prepare for a visit from the Ecology Inspector. The Inspector hopes to enlist the aid to the ThunderCats in capturing Two-Time, an intergalactic land poacher who has been stealing entire land masses with his geodesic vessel.
A rare lunar eclipse casts an eerie pale over the new ThunDERa. The eclipse opens a portal where the exiled Shadowmaster contacts the Ancient Spirits of Evil.
Mumm-Ra unveils his latest weapon, the Babylonian Barbarian Boiler, to destroy the ThunderCats. The Boiler emits a beam that rapidly melts anything it touches.
Captain Cracker attacks bounty hunter Captain Bragg, who is holding the exiled Luna-Taks prisoner, and frees the Luna-Taks in order to have them help him return Third Earth to a pirate's paradise.
In an effort to reach a distressed Thundarian spaceship, the ThunderCats must use all of their supplies of Thundrillium to fuel the Feliner for a deep-space voyage.
The tremors that previously threatens to destroy the new ThunDERa begin again when Jagara loses control of the gyroscope. The ThunderCats bring in a gyroscope specialist robot named Screw-Loose.
Wilykat and Wilykit discover the Golden Sphere of Setti, an ancient artifact that once belonged to Mumm-Ra. The sphere magnifies his power by four, making him more powerful than the Ancient Spirits of Evil.
The Ancient Spirits of Evil provide Mumm-Ra with a Mirror Wraith, which can take the form of any shape and travel through space using mirrors as portals. Meanwhile, an escape pod containing a Thundarian child named Leah is rescued by the ThundarCats.
Mumm-Ra realizes he must destroy the new ThunDERa in order to destroy the ThunderCats, so he travels to the Great Beneath and blasts the gyroscope into rapid decay.
The ThunderCats are determined to stay on the new ThunDERa despite its unstable environment. Meanwhile, Mumm-Ra summons Grune the Destroyer to help him destroy the ThunderCats.
The Ancient Spirits give Mumm-Ra until sundown to destroy the ThunderCats or be banished from Third Earth forever.
Mumm-Ra's mentors, the Ancient Spirits of Evil, threaten to relinquish Mumm-Ra's rule over Third Earth if he fails to destroy the ThundarCats.
Following up on a rumor, the ThunderCats take the Feliner to ThunDERa where supposedly a piece of the Treasure of ThunDERa lies within the Caverns of Cold. Mumm-Ra watches them in his cauldron and concocts a trap for them.
Snarf accidentally discovers the Bracelet of Power has the power to control the ThunderCats. Gradually, he starts to coerce the ThunderCats to do his bidding. Snarf then loses the bracelet to Mumm-Ra.