Episode 1

After saving a old man named Tyron from the rat-like Groundlings, Thundarr, Ariel and Ookla learns 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.

Episode 2

Thundarr, Princess Ariel, and Ookla encounter a train carrying Death Flowers (whose pollen can hypnotise both humans and Moks) being transported by the Carocs (a race of crocodile people) to a wizard.

Episode 3

The evil wizard Mindok lost his body in the Great Cataclysm 2000 years earlier, although his brain survived. He, General Zoa, and Zoa's minions seek out cryogenically frozen 20th-century scientists called "Ice People" in a plot to build Mindok a new body for his brain.

Episode 4

The evil wizard Morag and his raiders attack a cruise ship village to kidnap its inhabitants and steal their life essence.

Episode 5

Thundarr, Princess Ariel, and Ookla come to the aid of the Mok Chieftain Oblach against Captain Kordon, Queen of the River Pirates, who is after the Mok's hidden treasure and intends to use the "fire lances of the ancients" to get it.

Episode 6

Thundarr, Princess Ariel, and Ookla come to the aid of a race of amphibious Amazons led by the deposed Queen Diona who has been usurped by Stryia, an evil half-human, half-shark wizard-queen who plans to conquer both the land and seas with her shark legion army.

Episode 7

Zevon is the leader of the Brotherhood of Night, a tribe of werewolves that can add anyone to their ranks by touching them and is also targeting the evil wizard Infernus hoping to make the pack completely invincible.

Episode 8

Thundarr, Princess Ariel, and Ookla are caught up in a battle between the wizards Sholow and contestants Basim, Skorpos and Chom who seek the Helmet of Power. Thundarr ends up having to side with the wizard Sholow when he threatens a group of villagers.

Episode 9

Simius and his fellow Man Apes assemble salvaged parts of a movie studio's giant robotic gorilla in a plot to terrorize the local villagers.

Episode 10

A spaceship containing an alien vampire lands on Earth. The alien captures Princess Ariel and all the villagers in the ruins of Lakeside Amusement Park hidden under the snow and ice of the Rockies as a source of its food.

Episode 11

The evil wizard Crom threatens a tribe of humans at the Alamo. They can protect themselves by using a sophisticated Guardian machine that utilizes flying robot drones that can disable the wizard's laser tanks. However, it blows a circuit and cannot be replaced as circuits are no longer produced. Their only hope is to infiltrate Crom's lair in order to use his moon dial, which sends them to Old Earth. In the 20th century, Thundarr, Ookla and Ariel are aided by a little girl named Samantha, who helps them obtain a fresh circuit. The trio return to New Earth and prepare for battle with Crom, but are glad they had a chance to see the preapocalyptic world.

Episode 12

The evil wizard Kublai seeks the Golden Scepter of the Yantzee (the only item which can strip him of his magic) and terrorizes the villagers of San Francisco's Chinatown in the process. When Thundarr thwarts his initial attempts, the wizard recruits another barbarian named Zogar to engage him in battle while Kublai tries again to find the scepter.

Episode 13

Judag is a bitter, escaped 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.