Here's the answer, and don't read it if you haven't seen the movie:
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Now I can't think of any of the character names, so I'll identify them by the actors who played them: The Mark Wahlberg character gets to go back in time to Earth via the capsule that the chimp showed up in. Leaving behind the general character played by Tim Roth. Roth hates Wahlberg, and would love nothing better than to get revenge. So he does. By dredging up Wahlberg's original capsule out of the swamp, repairing it, and using the knowledge gained by the crashed space station's computer, he is able to go back even further in time to Earth, mess with its history enough to cause apes to become dominant, knowing that when Wahlberg shows up again everything will be changed. Voila! Revenge.