The folks over at CHUD got their hands on a copy of the current script by Amanda Silver and Rick Jaffa.and says the duo put in lots of little nods to the original "Conquest of the Planet Of The Apes" from which much of the premise is based, and to the original 1968 "Apes".
The general story has a doctor trying to cure Alzheimer's. After his research is shut down, he takes home and raises Caesar, the child of his most promising chimp experiment subject. Caesar continues to evolve and soon leads an army of apes in an uprising around the same time humanity is hit by a catastrophe.
One of the more interesting touches are numerous references to the launch and disappearance of the Icarus led by Colonel Taylor, the lead character and ship which crashed on the future Earth in the original Apes played by Charlton HestonThe other is that the cataclysm that hits humanity ties in to the genetic mutation and explains not just how the apes evolve enough to lead an uprising, but why the apes in the original series looked nothing like the modern apes of today.