First of all, some of the run downs of this movie are thought up by me (such as in Thade's Revenge to your right), as it's just what I thought could be the only way things could happen the way they did. I'm sure there will be a sequel to explain how everything REALLY happened, but this is my own personal damned opinion, so take it as that.

Part 1

Let's start from the beginning of the actual planet, and shorten the story up. The spaceship Oberon just lost two space pods, one with a chimp on a mission and one with a human looking for the lost chimp, in an electrical storm, so it follows them into the storm to find them. The electrical storm sends the Oberon throusands upon thousands of years into the past. The Oberon crash lands on a planet and they find it uninhabited.
The Oberon had around 40 or so different primates (chimps, gorillas, orangutangs) on board. These apes help the Oberon crew start a new civilization. One day, a chimp known as Cemose gets the other apes riled up by telling them the humans are making them slaves (the apes were smarter than anyone ever thought, and knew how to talk all along, but just never did because they thought of themselves as slaves), and Cemose and the others ran the humans off. Thousands of years later, Cemose is now a biblical figure and is prayed to, and the apes have all evolved. The humans that were spawned from the Oberon crew are either slaves or line in tribes outside of the Ape city. Suddenly there's a crash landing on the planet.