While Galen and Virdon hunt down a band of murderous ape dragoons, the blind daughter of a murdered chimpanzee falls in love with Burke, unaware that he is human. While Galen tries to infiltrate the ranks of the dragoons, Burke & Virdon work with the local gorilla police to bring down the renegades. With the dragoons about to launch a massive campaign against the human populations in the area, Galen, Burke & Virdon must work quickly if they are to keep the countryside safe for apes and humans alike.
While staying with human farmers, Galen is stung by a scorpion. The farmer's boy, Gregor, rides a horse to town to fetch an antidote but is followed by gorillas and arrested for riding. The three appeal to the Prefect Barlow (The Gladiators) who tells them that if Virdon rides in the upcoming horse race against Urko's jockey, and wins, he'll release Gregor. But things are complicated when Urko decides to oversee the race personally. Things are made even worse when Gregor's father, Martin, strikes a deal with Urko to ensure his victory.
When Burke is captured by the apes, Zaius gives a chimpanzee scientist, Wanda, the go-ahead to experiment on him using newly discovered brain washing techniques. Meanwhile, Galen & Virdon seek aid from Galen's parents who, reluctantly, give them shelter while they search for Burke. Burke is subjected to a brutal interrogation, in the meantime, and could break at any moment. Knowing that Galen & Virdon will come to try and rescue Burke, Urko takes the opportunity to plant a trap for the last of the fugitives.
When a tyrannical gorilla, Aboro, begins raiding the farms of local humans, the three fugitives and a young human, named Mikal, attack one of his caravans and take back the loot. Aboro retaliates by killing Mikal at his farm. When Galen appeals to his cousin, the Prefect Augustus, Aboro reveals the fruits of his payoffs to Central City: he has been apointed prefect in Augustus' place. In an attempt to foil Aboro's ascension, the three must convince Urko that the new gorilla prefect is guilty of bribary.
When Trion, a village of humans, is struck with disease, a chimpanzee doctor, Zoran, is dispatched by the High Council to investigate the incident. But the three fugitives arrive in Trion before him and identify the illness as malaria. Burke & Virdon manage to convince Zoran to take their approach to cure the disease. But Zoran's ability to convince the High Council against Urko's solution, burning the village to the ground, may not be as successful. If the cure is not discovered in time, every man woman and child in Trion will either die of disease, or be burned to death by the apes.
Virdon and Burke are captured by human slavers of Borak, who sell other humans to the apes. According to their mythology, the gods punish all those who do not abide by this tradition, fatally. While Virdon and Burke are prepared to be given to the apes as slaves for the mines, Galen continues to try and free his compatriots. But Viron & Burke must also learn the secrets of the local deities, and the darker secretes of Borak's master or else countless numbers of humans and apes alike will perish.
The fugitives spot a renegade human, named Leuric, flying a hang glider and being pursued by the gorilla police. While hiding Leuric from the patrols, the hang glider is brought before the High Council and becomes the interest of a chimpanzee scientist, Carsia. Leuric is captured by the gorillas and brought before Carsia, who gives him the opportunity to continue his work on his "flying machine". Meanwhile, Galen and the others infiltrate the facility to free Leuric and, in the process, learn of Carsia's murderous intentions for Leuric's hang glider.
