Thundarr, Princess Ariel, and Ookla escort a man who is carrying a magical black pearl that can defend against the two-faced wizard Gemini and his Groundlings (a race of mutated rat people). The man needs the pearl to protect the inhabitants of the village of "Manhat", which is actually the ruins of Manhattan.
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 that they work for. The episode introduces Tye, a swamp-urchin, who agrees to aid Thundarr on the basis that he capture the train and give it to her. Tye would reappear in Season 2's "Last Train to Doomsday".[10]
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.
The evil wizard Morag and his raiders attack a cruise ship village to kidnap its inhabitants and steal their life essence.
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 Moks' hidden treasure and intends to use the "fire lances of the ancients" to get it. Thundarr learns that these "fire lances" are actually 20th century torpedoes and rallies the Moks to defend the ruins of a U.S. Navy base against being captured by the River Pirates.
Thundarr, Princess Ariel, and Ookla come to the aid of a race of amphibious Amazons whose queen has been usurped by Stryia, an evil witch who plans to conquer both the land and seas with her shark legion army.
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.
Thundarr, Princess Ariel, and Ookla are caught up in a battle between the wizards Showlow 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.
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.
A spaceship containing an alien vampire lands on Earth. The alien captures Princess Ariel and some villagers in an amusement park's ruins as a source of food.
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.
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.
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.
The wizard Skullus and his soldiers are enslaving villagers living in a ruined oil refinery and using them to attack the fortress of his enemy, the equally evil wizard Octagon.
When coming to the aid of an escaped slave, Thundarr, Princess Ariel, and Ookla are captured by robots working for the multi-eyed wizard Lord Argoth who wants Ariel as his bride.
The trio investigate a sector called the Mystery Zone where several ships get wrecked on an island. They learn the evil witch Circe is responsible as she needs a young sorceress to overcome a curse in which she will turn to stone if she leaves the island. When Ariel arrives with Thundarr and Ookla, Circe gets her opportunity as she switches bodies with her and becomes a threat to the others as she tries to leave the island.
After being defeated by Thundarr, the evil wizard Sarott finds a research lab that holds the miniaturized City of Thieves. Its ruler Vortak promises Sarott a free rein to use the city's advanced army to enslave humans and other wizards if he can restore it to normal size. To do so, he'll need the Gauntlet of Power which can boost his magic to enlarge the city.
Thundarr, Ookla, and Ariel are in pursuit of Janus after he and a race of hawk mutants attack villages and the train route of Tye (the former swamp urchin from "Harvest of Doom"). The group is in for a surprise when it turns out Janus is actually Gemini (the two-faced wizard from "Secret of the Black Pearl") in disguise seeking revenge on Thundarr. Tye, from "Harvest of Doom", returns as a train driving "businesswoman".
During a battle with Yando (a supposed wizard with unusual magic), Thundarr is struck by red negative lightning which significantly diminishes the power of his Sunsword. The weapon can be restored at the nearby Pool of Power, but it is stolen by Yando who seeks to have the Sunsword's power for himself.
Thundarr's friend Thorac is accused of stealing a village's fuel and is about to receive a death sentence (by being boiled alive over a geyser) when the barbarian rescues him. Thorac is granted a reprieve when Thundarr and the group investigate the crime, eventually learning the town's sheriff Korb is in league with the evil wizard Artemus. Artemus had stolen the fuel to power his Death Ship and gain the approval of the Council of Wizards.
Thundarr, Princess Ariel, and Ookla battle the evil wizard Vashtarr when he steals the Crystal of Prophecy that can give the details of his downfall. When it shatters in his efforts to retrieve it, the prophecy is foretold as they learn three women will unite to defeat him. One is Maya, an element-shifter buried in the ruins of the old city of Endorr. Another is Cinda, a hermitic barbarian living in the Canyon of Death whose staff grants her great strength. The last is Valerie Storm, a fashion model from Old Earth who is abducted and taken prisoner by Vashtarr himself.
