Thundarr, Princess Ariel, and Ookla escort a man who is carrying a magical black pearl that can protect its possessor from evil magic to Manhat's (formerly New York City's smallest borough) ruins while evading the two-faced wizard Gemini and his Groundlings (a race of rat people). (Gemini returns in Last Train to Doomsday).
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 the swamp urchin who returns in Last Train to Doomsday.
The evil wizard Mindok lost his body in the Great Catalysm 2000 years ago, although his brain remained immortal. He, General Zoa, and Zoa's minions seek out cryogenically frozen Old Earth scientists named "Ice People" in a plot to build Mindok a new body to house his brain.
Thundarr, Princess Ariel, and Ookla come to the aid of the Mok Chieftain Oblach. Captain Kordon the Queen of the River Pirates is after the Moks' hidden treasure and she intends to use the "fire lances of the ancients"-20th century missiles- to get it.
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 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. Outside of a plot to assimilate Thundarr into his pack, he 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 four wizards who each seek to claim the Helmet of Power. Thundarr ends up having to side with the wizard Sholow when he threatens the city's villagers.
The evil wizard Khromm 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. But when it blows a circuit, Thundarr and the group must use Khromm's moon dial to journey into the past to get the necessary replacement part for the Guardian. This enables Thundarr's crew to see Old Earth and then return to their own time to save the village from Khromm.
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 Zogar, another barbarian 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 an alleged 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 gang investigate an area 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 in her own body. 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 inside Ariel's body.
After being defeated by Thundarr, the evil wizard Sarott stumbles into 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 and his men are in pursuit of Janus after he and a race of Hawkmen attack some villagers 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 in disguise seeking revenge on Thundarr.
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. The first is Maya, an element-shifter buried in the ruins of the old city of Endor where she once ruled. The second is Cinda, a barbarian residing 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.