Question: To prevent spoilers/plot leaking to the public, Tim Burton made five endings to keep people guessing. Is there anywhere I can see any of the other four?
Answer: There were five different endings to the movie and late actor Michael Clarke Duncan saw them all. So far, no website seems to have all five endings. Just the one we're familiar with.
Answer: You might be mistaken, there was only ever one ending shot for this film: the ending we all saw at the Lincoln Memorial. There were different planned endings (one was a similar ending to the theatrical but set at Yankee stadium with apes playing baseball) that were each rejected for various reasons. The ending we see is the one that is in the script.
Question: Can someone please explain how the apes ended up taking over present-day Earth since the future apes never got hold of the time machine? I can't find anyone who can make heads or tails of it.
Chosen answer: Tim Burton has been quoted MANY times as saying it isn't supposed to make sense. Best guess is Leo travelled not just into the future, but into another dimension as well. Ironically, this ending is far more true to Peirre Boulle's original ending than the first Apes movie.
Answer: I have, if not an answer, then a sharpening of the question. A number of fanboys have suggested Thade retrieved Leo's pod from the bottom of the lake, then used it to travel into the MagnaStorm, thereby reaching Earth centuries before Leo's arrival, and inciting Earth Apes to rebel. The problem with This explanation is, once you get past how helpless the Apes are in water, How did Thade, a person who comes from a society without even gunpowder level technology, Repair A Spaceship?! Nevermind learn to use it?!?!?.
Question: Shortly after Leo enters a pod to try and save Pericles, the crew of the Oberon receive a distress signal from an old man. Who exactly was that guy?
Answer: It's Lt. General Vasich. It's a message from the future--or from the past depending on how you read the timeline--made after they attempt to rescue Captain Davidson and get thrown in time to well before Leo arrives on the other side. That's why Vasich looks so confused after seeing the message.
Question: When Pericles is sent out into space, he enters the wormhole, Leo next and then the Oberon. So how did the Oberon land first, then Leo and Pericles last?
Answer: The anomaly they encountered was not merely a spatial wormhole, it was a rift in time. The order in which they entered the time-rift didn't matter; they could exit the rift in any random order, minutes or months or millennia apart.
Answer: It is understood the order-of-exit is reversed to the order of Entry, although not stated.
Question: How exactly was Semos able to organize a rebellion against the humans, since he was just an ordinary ape who was trained for whatever assignment he would be needed for?
Answer: The dialogue recorded by one of the survivors of the Oberon tells that the apes, particularly Semos are much smarter than they had ever realized. He was not ordinary, he was the offspring of two chimps that had been genetically modified for increased intelligence. Semos had intelligence near or equal to humans.
Answer: To prevent anyone else from learning that Leo came from space. After Pericles' ship crashed, there was a prophecy of a second coming of Semos, the founder of Ape civilization. Thade wants to kill all humans, so if anyone found out, it would be considered a sign and the council might consider making peace with the humans.
Captain Defenestrator