Season 2

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 a mummy-like 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.