Death Flowers, the pollen of which numbs the human will, are being harvested by Carocs, a fierce warrior race of humanoid crocodiles who are serving an evil Wizard. After the first encounter with the Carocks, Thundarr and Ariel are thrown into a snake pit and Ookla is captured and set to work in the Death Flower fields.
After escaping the snake pit, Thundarr and Ariel encounter Tye, a swamp urchin who agrees to help if the Carocs' train is given to her as payment. Tye leads Thundarr and Ariel down the river and through a golden Aztec pyramid into the valley beyond. Ookla, under the mind-numbing spell of the death flowers, does battle with Thundarr alongside the Caroc guards. Ookla and the Carocs fall to Ariel's magic as Thundarr sets the Death Flower fields ablaze with his Sunsword, destroying the deadly harvest.
With Ookla freed from the Death Flowers' spell, the three heroes and Tye escape the valley through the pyramid and follow the Death Flower train on horseback. Eventually they bring the train to a halt, defeat the Carocs and destroy the train's deadly cargo. Thundarr and Ookla repair the damage they did to the tracks in the final battle and turn the train over to Tye as they agreed.