In the year 2125 A.D., four USNSA astronauts named Martinez, Romulus, Sophie, and Ulysses got onboard a ship called Cassiopeia. They went into space and began cryogenic sleep on December 4th.
During their absence from Earth, two human armies had a "war to end all wars". The elite of the USNSA took refuge in the underground city named "Ark". Earth's surface was damaged by fire and radiation. Surviving humans desperately wanted to repair the landscape.
In 2274, the first results of a research project called "Accelerated Evolution" were produced. Five years later, an ape worker was used to build "Neocities". By the year 2317, there were apes working everywhere. They grew very unhappy with their status in society. Three years later, the apes revolted. Work began on a second "Ark" project. It took the apes nine years to defeat the humans and become the dominant species.
At that time, ten thousand humans lived underground, and they cut off all contact with the surface. Years later, a girl named Valis foretold a prophecy before she died. She spoke of a savior who would come down from space and fight for the freedom of humankind. A group of humans led by the one called Ellia returned to the surface in an attempt to reconquer the planet. They failed. Ellia then decided to divide the Ellisians into three tribes. She gave a part of a key to each tribe leader: the gold part to Ezekiel, the silver part to Tomas, and the glass part to John. The tribes of John and Tomas died out, but Ezekiel's tribe survived. The silver and glass parts were in the hands of the apes.
Generations later, on October 18th, 3889, Cassiopeia returned. Upon their arrival, three of the astronauts discovered that Martinez had died do to a malfunction on the ship. They walked through a desert until they saw humans in trees and found themselves in the middle of a manhunt. The hunters were apes. Romulus and Sophie were shot to death. Ulysses survived and was taken to a research center, where he was studied by a chimpanzee named Doctor Zira. He escaped and met the human resistance of Ellisians. Among the resistance fighters were Nova and her brother Mathias.
Ulysses learned of General Ursus' plan to use research done by Professor Cornelius, Zira's husband, to modify gorilla DNA so that gorillas could be superior to all other apes. Ulysses told Cornelius about this, and the chimpanzee scientist agreed to destroy his research. After the resistance leader Jonah died, Mathias took his place. Ulysses recovered the two parts of the key that had been lost. All three pieces formed a map that led Ulysses to a tunnel of the Akanites. There, he found a recording detailing Earth's history and denied the preconceived notion that he was the messiah who was destined to fight for humanity. He met with the five ape leaders Zaius, Ursus, mandrill General Rakham, a chimpanzee named Xander, and a baboon named Beollu to free Nova after she had been captured. He informed them of Ursus' plan to abuse his power. After Ursus' arrest, Zaius allowed Nova and Ulysses to leave as long as they stayed far away. And so, they rode a horse away from Ape City. Zaius believed that he prevented a rebellion, but he was wrong...