After saving a old man named Tyron from the rat-like Groundlings, Thundarr, Ariel and Ookla learn that the Groundlings are in search of The Black Pearl, which the evil wizard Gemini fears it's power. Thundarr, Ariel and Ookla agrees to deliver the Black Pearl to the village of Manhat (the ruins of Manhattan). But Ariel is captured and taken to Gemini's tower and Gemini demands that Thundarr and Ookla gives him the Black Pearl or Ariel will die.
Thundarr and his companions come across a band of crocodile men called Carocs who are breeding Death Flowers, capable of controlling human minds, for an evil wizard. When Ookla is captured and forced to work in the Carocs' fields, Thundarr and Ariel must rely on a swamp urchin named Tye to help them rescue Ookla and destroy the flowers.
Thundarr, Ariel and Ookla discover the ancient NASA Space Center facility in the ruins of Cape Canaveral in which three scientists hibernate in refrigerated boxes; they survived the destruction of Earth. Unfortunately, they awaken into a world of wizards, and one in particular, Mindok, has plans for them - they'll help him build a war machine with which to conquer what's left of the world, whether they want to or not.
Captain Corden has her eye on the legendary treasure of the Moks, a supposed fortune in gold hidden somewhere within the Mok city. To get it, she has assembled a fleet of small ships armed with missiles recovered from a pre-cataclysm Navy base. She'll overwhelm even the powerful Moks with these weapons unless Thundarr, Ariel and Ookla can stop her!
The Brotherhood of Night, a sinister collection of werewolves created from hapless villagers in Washington DC's ruins, intends to make itself invincible by adding the wizard Infernus to its number! Thundarr actually finds himself fighting on the side of a wizard for once, but when Infernus is transformed, Thundarr gets the kind of mistreatment he has come to expect from wizards.
Sholow, a dangerous wizard who abides in the ruins of Las Vegas, seizes a large number of innocent people and suspends them in a magical cage! Unless Thundarr retrieves The Helmet of Power, an artifact that magnifies magic enormously, Sholow will kill the innocent hostages. Thundarr reluctantly agrees, and must defeat the forces of Sholow, Scorpos, and Chomm, other wizards who also seek the relic. Then he must figure out how to free the hostages without surrendering the magical helmet to the evil Sholow!
Crom, an evil wizard threatens a tribe of humans at the Alamo. They can protect themselves as they use a sophisticated Guardian machine which utilizes flying robot drones that can disable the wizard's laser tanks. Unfortunately it blows a circuit and cannot be replaced. Their only hope is to break into Crom's lair and use his moon dial, which can send them to Old Earth. In the 20th century, Thundarr, Ookla and Ariel rely on a little girl, Samantha, who helps them obtain a fresh circuit. The trio return to New Earth and prepare for battle with Crom.
The evil wizard Kublai seeks the Golden Scepter of the Yantzee - the only item which can strip him of his magic. In the mean time Kublai terrorizes the villagers of San Francisco's Chinatown. When Thundarr thwarts his initial attempts, the wizard recruits another barbarian named Zogar to challenge him in a battle while Kublai tries again to find the scepter.
Judag is a bitter, a former slave of an evil wizard who plans to awaken a sleeping demon that allegedly can grant whoever wakes it the powers of 1,000 wizards. It is up to Thundarr to prevent Judag from accomplishing this mission.