In the Saturday morning version, astronaut Bill Hudson and his crew, Jeff Carter and Judy Franklin, were on a mission when their craft, the Venture, got caught in a time-vortex and crash landed in the year A.D. 3979. (about 1000 years later than in the film). Unaware that they had actually landed on earth, Bill and company found themselves in a society where intelligent apes were the rulers and humans were treated as a lesser species; serving as pets, servants, and sport for hunters. Mankind had in fact reverted to a primitive and uncivilized version of itself, unable even to speak, and was relegated to a separate area called New City. Despite knowledge that humans had once ruled the earth was lost to all but a handful of ape scholars, humans were still viewed as a threat and a menace by some apes, who called for the their eradication.

Humans were subjected to scientific experiments by an ape named Dr. Zaius, the ape community's scientific leader, with the assistance of two simian underlings, Cornelius and Zira. Bill, like the Charlton Heston character in the film, was captured, but won the sympathy of Cornelius and Zira when they realized that he had the ability to speak. Aware that the human's ability to talk made him a prime candidate for brain surgery, Cornelius and Zira helped him to escape.

Bill eventually reunited with his fellow astronauts and the three continued to struggle for survival in a world where they were not welcome. Along with Dr. Zaius, Cornelius and Zira, other characters from the film were regulars on the cartoon, like military leader General Urko and human female Nova.